From e2dec6afd3740c352da91b1b5a5cef5435ca9a24 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 20 Nov 2019 23:54:46 +0100
Subject: [PATCH 01/42] Added heudiconv link

---
 phys2bids/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 1bbba65ce..4d0802909 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -80,7 +80,7 @@ def load_heuristic(heuristic):
 
     References
     ----------
-    Copied from nipy/heudiconv
+    Copied from [nipy/heudiconv](https://github.com/nipy/heudiconv)
     """
     if os.path.sep in heuristic or os.path.lexists(heuristic):
         heuristic_file = os.path.realpath(heuristic)

From f5dfaf0ebb1c90eab4780911672e7e06175c6afc Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 20 Nov 2019 23:59:39 +0100
Subject: [PATCH 02/42] Added main call

---
 phys2bids/phys2bids.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index e729ff1fc..3fac9bc66 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -276,3 +276,7 @@ def _main(argv=None):
         print_json(outfile, samp_freq, time_offset, options.table_header)
         print_summary(options.filename, options.num_tps_expected,
                       num_tps_found, samp_freq, time_offset, outfile)
+
+
+if __name__ == '__main__':
+    _main()
\ No newline at end of file

From 89240f90b93679102ebb6956848af3fc8d8ebdb1 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 01:11:55 +0100
Subject: [PATCH 03/42] Started writing classes for phys2bids

---
 phys2bids/physio_obj.py | 66 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 phys2bids/physio_obj.py

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
new file mode 100644
index 000000000..4548ec0f0
--- /dev/null
+++ b/phys2bids/physio_obj.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+
+"""
+I/O objects for phys2bids
+"""
+
+import numpy as np
+
+
+class phys_io():
+    """
+    Parent class for i/o physio objects.
+
+    Properties
+    ----------
+    ch_name: (ch, ) list
+        List of channel names - one per channel
+    units: (ch, ) list
+        list of channel frequencies - one per channel
+    """
+    def __init__(self, ch_name, units):
+        self.ch_name = ch_name
+        self.units = units
+
+
+class phys_input(phys_io):
+    """
+    Main input object for phys2bids.
+    Contains the schema to be populated.
+
+    Properties
+    ----------
+    timeseries : (ch, [tps]) list 
+        List of numpy 1d arrays - one for channel.
+        Contains all the timeseries recorded.
+        Supports different frequencies!
+    freq : (ch, ) list
+        List of floats - one per channel.
+        Contains all the frequencies of the recorded channel.
+        Support different frequencies!
+    """
+    def __init__(self, diff_timeseries, diff_freq, ch_name, units):
+        super().__init__(ch_name, units)
+        self.timeseries = diff_timeseries
+        self.freq = diff_freq
+        
+
+class phys_output(phys_io):
+    """
+    Main output object for phys2bids.
+    Contains the schema to be exported.
+
+    Properties
+    ----------
+    timeseries : (ch x tps) :obj:`numpy.ndarray`
+        Numpy 2d array of timeseries 
+        Contains all the timeseries recorded.
+        Impose same frequency!
+    freq : float
+        Shared frequency of the object.
+    """
+    def __init__(self, timeseries, freq, ch_name, units):
+        super().__init__(ch_name, ch_name, units)
+        self.timeseries = timeseries
+        self.freq = freq
+        
\ No newline at end of file

From e936b582647059e513660b8ae397cdc410aec335 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 15:38:56 +0100
Subject: [PATCH 04/42] Start writing methods

---
 phys2bids/physio_obj.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 4548ec0f0..45a037df5 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -6,6 +6,14 @@
 
 import numpy as np
 
+def is_valid(var, type, list_type):
+    """
+    Checks that the var is of a certain type.
+    If type is list and list_type is specified,
+    checks that the list contains
+    """
+
+
 
 class phys_io():
     """
@@ -30,7 +38,7 @@ class phys_input(phys_io):
 
     Properties
     ----------
-    timeseries : (ch, [tps]) list 
+    timeseries : (ch, [tps]) list
         List of numpy 1d arrays - one for channel.
         Contains all the timeseries recorded.
         Supports different frequencies!
@@ -43,7 +51,7 @@ def __init__(self, diff_timeseries, diff_freq, ch_name, units):
         super().__init__(ch_name, units)
         self.timeseries = diff_timeseries
         self.freq = diff_freq
-        
+
 
 class phys_output(phys_io):
     """
@@ -53,7 +61,7 @@ class phys_output(phys_io):
     Properties
     ----------
     timeseries : (ch x tps) :obj:`numpy.ndarray`
-        Numpy 2d array of timeseries 
+        Numpy 2d array of timeseries
         Contains all the timeseries recorded.
         Impose same frequency!
     freq : float

From 9bc82f405b5ded060c3791d50a692acf021ac8ee Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 17:19:45 +0100
Subject: [PATCH 05/42] Turned a string into f string

---
 phys2bids/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 4d0802909..effb9bcdd 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -32,7 +32,7 @@ def check_file_exists(file, hardexit=True):
     Check if file exists.
     """
     if not os.path.isfile(file) and file is not None:
-        raise FileNotFoundError('The file ' + file + ' does not exist!')
+        raise FileNotFoundError(f'The file {file} does not exist!')
 
 
 def move_file(oldpath, newpath, ext=''):

From afad556c999bc233bf00b2b582b64f508458edd1 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 18:47:34 +0100
Subject: [PATCH 06/42] Finished object organisation

---
 phys2bids/physio_obj.py | 83 +++++++++++++++++++++++++++++++++++------
 1 file changed, 72 insertions(+), 11 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 45a037df5..6fa9fbb97 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -1,18 +1,74 @@
 #!/usr/bin/env python3
 
 """
-I/O objects for phys2bids
+I/O objects for phys2bids.
 """
 
-import numpy as np
+from numpy import ndarray, shape
 
-def is_valid(var, type, list_type):
+
+def is_valid(var, type, list_type=None, return_var=True):
     """
     Checks that the var is of a certain type.
     If type is list and list_type is specified,
-    checks that the list contains
+    checks that the list contains list_type.
+    Input
+    -----
+    var:
+        Variable to be checked.
+    type: type
+        Type the variable is assumed to be.
+    list_type: type
+        As type.
+
+    Output
+    ------
+    var:
+        Variable to be checked (same as input).
     """
+    if not isinstance(var, type):
+        raise AttributeError('Something went wrong while populating physio_io!')
+
+    if type is list and list_type is not None:
+        for element in var:
+            is_valid(element, list_type, return_var=False)
+
+    if return_var:
+        return var
+
+
+def has_data_size(var, data, token):
+    """
+    Checks that the var has the same dimension of the data
+    If it's not the case, fill in the var or removes exceding var entry.
+    Input
+    -----
+    var:
+        Variable to be checked.
+    data: (ch, [tps]) list or :obj:`numpy.ndarray`
+        Actual timeseries data.
+    token:
+        What to be used in case of completion.
+
+    Output
+    ------
+    var:
+        Variable to be checked (same as input).
+    """
+    if isinstance(data, list):
+        data_size = len(data)
+    elif isinstance(data, ndarray):
+        data_size = data.shape[0]
+    else:
+        raise Exception('Something went wrong assessing data size')
+
+    if len(var) > data_size:
+        var = var[:data_size]
+
+    if len(var) < data_size:
+        var = var + [token] * (data_size - len(var))
 
+    return var
 
 
 class phys_io():
@@ -27,8 +83,8 @@ class phys_io():
         list of channel frequencies - one per channel
     """
     def __init__(self, ch_name, units):
-        self.ch_name = ch_name
-        self.units = units
+        self.ch_name = is_valid(ch_name, list, list_type=str)
+        self.units = is_valid(units, list, list_type=str)
 
 
 class phys_input(phys_io):
@@ -49,8 +105,12 @@ class phys_input(phys_io):
     """
     def __init__(self, diff_timeseries, diff_freq, ch_name, units):
         super().__init__(ch_name, units)
-        self.timeseries = diff_timeseries
-        self.freq = diff_freq
+        self.timeseries = is_valid(diff_timeseries, list, list_type=ndarray)
+        self.freq = has_data_size(is_valid(diff_freq, list,
+                                           list_type=(int, float)),
+                                  self.timeseries, 0)
+        self.ch_name = has_data_size(self.ch_name, self.timeseries, 'missing')
+        self.units = has_data_size(self.units, self.timeseries, '[]')
 
 
 class phys_output(phys_io):
@@ -69,6 +129,7 @@ class phys_output(phys_io):
     """
     def __init__(self, timeseries, freq, ch_name, units):
         super().__init__(ch_name, ch_name, units)
-        self.timeseries = timeseries
-        self.freq = freq
-        
\ No newline at end of file
+        self.timeseries = is_valid(timeseries, ndarray)
+        self.freq = has_data_size(is_valid(freq, (int, float)), [1], 0)
+        self.ch_name = has_data_size(self.ch_name, self.timeseries, 'missing')
+        self.units = has_data_size(self.units, self.timeseries, '[]')

From dcb24197d2a767b3898d49ca3abda24f996a6dba Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 22:12:25 +0100
Subject: [PATCH 07/42] Just flake8ed the eof

---
 phys2bids/phys2bids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 3fac9bc66..f9ce661d1 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -279,4 +279,4 @@ def _main(argv=None):
 
 
 if __name__ == '__main__':
-    _main()
\ No newline at end of file
+    _main()

From 79acc2764fb84db512ebd53bbde1a47e87821633 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 22:58:37 +0100
Subject: [PATCH 08/42] Started writing interface for acq files

---
 phys2bids/interfaces/acq.py | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 phys2bids/interfaces/acq.py

diff --git a/phys2bids/interfaces/acq.py b/phys2bids/interfaces/acq.py
new file mode 100644
index 000000000..ea731a554
--- /dev/null
+++ b/phys2bids/interfaces/acq.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+phys2bids interface for acqknowledge files.
+"""
+from bioread import read_file
+
+from phys2bids.physio_obj import blueprint_input, blueprint_output
+
+
+def print_info_acq(filename, data):
+    """
+    Print the info of acq files
+    """
+    print(f'File {filename} contains:\n')
+    for ch in range(0, len(data)):
+        print(str(ch) + ': ' + data[ch].name)
+
+
+def populate_phys_input(filename, chtrig):
+    """
+    Populate object phys_input
+    """        
+
+    data = read_file(filename).channels
+    phys_input = blueprint_input()
+
+

From c6d69e378523771ea6400e8502fd2e7412350367 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 22:59:01 +0100
Subject: [PATCH 09/42] changed name of objects

---
 phys2bids/physio_obj.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 6fa9fbb97..acce68157 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# -*- coding: utf-8 -*-
 
 """
 I/O objects for phys2bids.
@@ -71,7 +72,7 @@ def has_data_size(var, data, token):
     return var
 
 
-class phys_io():
+class blueprint_io():
     """
     Parent class for i/o physio objects.
 
@@ -87,10 +88,10 @@ def __init__(self, ch_name, units):
         self.units = is_valid(units, list, list_type=str)
 
 
-class phys_input(phys_io):
+class blueprint_input(blueprint_io):
     """
     Main input object for phys2bids.
-    Contains the schema to be populated.
+    Contains the blueprint to be populated.
 
     Properties
     ----------
@@ -113,10 +114,10 @@ def __init__(self, diff_timeseries, diff_freq, ch_name, units):
         self.units = has_data_size(self.units, self.timeseries, '[]')
 
 
-class phys_output(phys_io):
+class blueprint_output(blueprint_io):
     """
     Main output object for phys2bids.
-    Contains the schema to be exported.
+    Contains the blueprint to be exported.
 
     Properties
     ----------

From b94def5ae28a19083b6a557aab4f73b0110355ee Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 21 Nov 2019 23:00:25 +0100
Subject: [PATCH 10/42] Started moving acq related code into proper interface
 file

---
 phys2bids/phys2bids.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index f9ce661d1..c389dc0f0 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -31,18 +31,13 @@
 
 from phys2bids import utils, viz
 from phys2bids.cli.run import _get_parser
+from phys2bids.interfaces import acq
 
 # #!# This is hardcoded until we find a better solution
 HEADERLENGTH = 9
 
 
 # #!# Different frequencies == different files!
-def print_info_acq(filename, data):
-    print('File ' + filename + ' contains:\n')
-    for ch in range(0, len(data)):
-        print(str(ch) + ': ' + data[ch].name)
-
-
 def print_info_txt(filename):
     with open(filename) as txtfile:
         header = [next(txtfile) for x in range(HEADERLENGTH - 2)]
@@ -145,7 +140,7 @@ def _main(argv=None):
         from bioread import read_file
 
         data = read_file(infile).channels
-        print_info_acq(options.filename, data)
+        acq.print_info_acq(options.filename, data)
     elif ftype == 'txt':
         header = print_info_txt(options.filename)
 
@@ -256,8 +251,8 @@ def _main(argv=None):
             if table_width < n_headers - ignored_headers:
                 print(f'Too many table headers specified!\n'
                       f'{options.table_header}\n'
-                      f'Ignoring the last'
-                      '{n_headers - table_width - ignored_headers}')
+                      f'Ignoring the last '
+                      f'{n_headers - table_width - ignored_headers}')
                 options.table_header = options.table_header[:(table_width + ignored_headers)]
             elif table_width > n_headers - ignored_headers:
                 missing_headers = n_headers - table_width - ignored_headers

From b603285c4dda0f7c24f9d3a48838fa863b376b97 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 13:01:06 +0100
Subject: [PATCH 11/42] Removed parent class, added start_time in output

---
 phys2bids/physio_obj.py | 25 ++++---------------------
 1 file changed, 4 insertions(+), 21 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index acce68157..3a022510b 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -72,23 +72,7 @@ def has_data_size(var, data, token):
     return var
 
 
-class blueprint_io():
-    """
-    Parent class for i/o physio objects.
-
-    Properties
-    ----------
-    ch_name: (ch, ) list
-        List of channel names - one per channel
-    units: (ch, ) list
-        list of channel frequencies - one per channel
-    """
-    def __init__(self, ch_name, units):
-        self.ch_name = is_valid(ch_name, list, list_type=str)
-        self.units = is_valid(units, list, list_type=str)
-
-
-class blueprint_input(blueprint_io):
+class blueprint_input():
     """
     Main input object for phys2bids.
     Contains the blueprint to be populated.
@@ -105,7 +89,6 @@ class blueprint_input(blueprint_io):
         Support different frequencies!
     """
     def __init__(self, diff_timeseries, diff_freq, ch_name, units):
-        super().__init__(ch_name, units)
         self.timeseries = is_valid(diff_timeseries, list, list_type=ndarray)
         self.freq = has_data_size(is_valid(diff_freq, list,
                                            list_type=(int, float)),
@@ -114,7 +97,7 @@ def __init__(self, diff_timeseries, diff_freq, ch_name, units):
         self.units = has_data_size(self.units, self.timeseries, '[]')
 
 
-class blueprint_output(blueprint_io):
+class blueprint_output():
     """
     Main output object for phys2bids.
     Contains the blueprint to be exported.
@@ -128,9 +111,9 @@ class blueprint_output(blueprint_io):
     freq : float
         Shared frequency of the object.
     """
-    def __init__(self, timeseries, freq, ch_name, units):
-        super().__init__(ch_name, ch_name, units)
+    def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.timeseries = is_valid(timeseries, ndarray)
         self.freq = has_data_size(is_valid(freq, (int, float)), [1], 0)
         self.ch_name = has_data_size(self.ch_name, self.timeseries, 'missing')
         self.units = has_data_size(self.units, self.timeseries, '[]')
+        self.start_time = start_time

From 70e69657489b464b5f8af4476cfde667334d9e7f Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 15:55:58 +0100
Subject: [PATCH 12/42] Adapted print_info to general input object, moved into
 utils, improved objects, started rewriting of main for objects

---
 phys2bids/interfaces/acq.py | 28 +++++++++++++-----------
 phys2bids/phys2bids.py      | 43 +++++++++++--------------------------
 phys2bids/physio_obj.py     |  9 ++++----
 phys2bids/utils.py          | 10 +++++++++
 4 files changed, 43 insertions(+), 47 deletions(-)

diff --git a/phys2bids/interfaces/acq.py b/phys2bids/interfaces/acq.py
index ea731a554..f6f358de8 100644
--- a/phys2bids/interfaces/acq.py
+++ b/phys2bids/interfaces/acq.py
@@ -9,21 +9,25 @@
 from phys2bids.physio_obj import blueprint_input, blueprint_output
 
 
-def print_info_acq(filename, data):
-    """
-    Print the info of acq files
-    """
-    print(f'File {filename} contains:\n')
-    for ch in range(0, len(data)):
-        print(str(ch) + ': ' + data[ch].name)
-
-
 def populate_phys_input(filename, chtrig):
     """
     Populate object phys_input
     """        
 
     data = read_file(filename).channels
-    phys_input = blueprint_input()
-
-
+    
+    freq = [data[chtrig].samples_per_second] * 2
+    timeseries = [data[chtrig].time_index, data[chtrig].data]
+    units = ['s', data[chtrig].units]
+    names = ['time','trigger']
+
+    k = 0
+    for ch in data:
+        if k != chtrig:
+            print(f'{k:02d}. {ch}')
+            timeseries.append(ch.data)
+            freq.append(ch.samples_per_second)
+            units.append(ch.units)
+        k += 1
+
+    return phys_input = blueprint_input(timeseries, freq, names, units)
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index c389dc0f0..27b999568 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -31,27 +31,12 @@
 
 from phys2bids import utils, viz
 from phys2bids.cli.run import _get_parser
-from phys2bids.interfaces import acq
+
 
 # #!# This is hardcoded until we find a better solution
 HEADERLENGTH = 9
 
 
-# #!# Different frequencies == different files!
-def print_info_txt(filename):
-    with open(filename) as txtfile:
-        header = [next(txtfile) for x in range(HEADERLENGTH - 2)]
-
-    del header[1:4]
-    del header[2]
-
-    print('File ' + filename + ' contains:\n')
-    for line in header:
-        print(line)
-
-    return header
-
-
 def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, outfile):
     start_time = -time_offset
     summary = (f'------------------------------------------------\n'
@@ -135,14 +120,16 @@ def _main(argv=None):
     utils.check_file_exists(infile)
     print('File exists')
 
-    # Read infos from file
+    # Read file!
     if ftype == 'acq':
-        from bioread import read_file
-
-        data = read_file(infile).channels
-        acq.print_info_acq(options.filename, data)
+        from phys2bids.interfaces.acq import populate_phys_input
     elif ftype == 'txt':
-        header = print_info_txt(options.filename)
+        raise Exception('txt not yet supported')
+    else:
+        raise Exception('File type not yet supported')
+
+    phys_input = populate_phys_input(infile, options.chtrig)
+    utils.print_info(options.filename, phys_input)
 
     # If file has to be processed, process it
     if not options.info:
@@ -157,16 +144,8 @@ def _main(argv=None):
                   f'Skipping BIDS formatting.')
 
         # #!# Get option of no trigger! (which is wrong practice or Respiract)
-        print('Reading trigger data and time index')
-        if ftype == 'acq':
-            trigger = data[options.chtrig].data
-            time = data[options.chtrig].time_index
-        elif ftype == 'txt':
-            # Read full file and extract right lines.
-            data = np.genfromtxt(options.filename, skip_header=HEADERLENGTH)
-            trigger = data[:, options.chtrig + 1]
-            time = data[:, 0]
 
+        # #!# MOVE THIS TO OBJECT METHOD! FROM HERE 
         print('Counting trigger points')
         trigger_deriv = np.diff(trigger)
         tps = trigger_deriv > options.thr
@@ -201,6 +180,8 @@ def _main(argv=None):
         time = time - time_offset
         # time = data[options.chtrig].time_index - time_offset
 
+        # #!# TO HERE
+
         utils.path_exists_or_make_it(options.outdir)
 
         viz.plot_trigger(time, trigger, outfile, options)
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 3a022510b..f661a1fe2 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -93,8 +93,9 @@ def __init__(self, diff_timeseries, diff_freq, ch_name, units):
         self.freq = has_data_size(is_valid(diff_freq, list,
                                            list_type=(int, float)),
                                   self.timeseries, 0)
-        self.ch_name = has_data_size(self.ch_name, self.timeseries, 'missing')
-        self.units = has_data_size(self.units, self.timeseries, '[]')
+        self.ch_name = has_data_size(ch_name, self.timeseries, 'missing')
+        self.units = has_data_size(units, self.timeseries, '[]')
+        self.ch_num = len(self.timeseries)
 
 
 class blueprint_output():
@@ -114,6 +115,6 @@ class blueprint_output():
     def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.timeseries = is_valid(timeseries, ndarray)
         self.freq = has_data_size(is_valid(freq, (int, float)), [1], 0)
-        self.ch_name = has_data_size(self.ch_name, self.timeseries, 'missing')
-        self.units = has_data_size(self.units, self.timeseries, '[]')
+        self.ch_name = has_data_size(ch_name, self.timeseries, 'missing')
+        self.units = has_data_size(units, self.timeseries, '[]')
         self.start_time = start_time
diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index effb9bcdd..937cebc46 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -35,6 +35,16 @@ def check_file_exists(file, hardexit=True):
         raise FileNotFoundError(f'The file {file} does not exist!')
 
 
+def print_info(filename, phys_object):
+    """
+    Print the info of the input files, using blueprint_input object
+    """
+    print(f'File {filename} contains:\n')
+    
+    for ch in range(2, phys_object.ch_num):
+        print(f'{(ch-2):02d}. {phys_object.ch_name[ch]} sampled at {phys_object.freq[ch]} Hz')
+
+
 def move_file(oldpath, newpath, ext=''):
     """
     Moves file from oldpath to newpath.

From 4497f82ddae691ef4a432b9c50c307a3038f35aa Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 19:59:53 +0100
Subject: [PATCH 13/42] Changed default tr

---
 phys2bids/cli/run.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phys2bids/cli/run.py b/phys2bids/cli/run.py
index 463b6ba57..803083315 100644
--- a/phys2bids/cli/run.py
+++ b/phys2bids/cli/run.py
@@ -89,7 +89,7 @@ def _get_parser():
                           dest='tr',
                           type=float,
                           help='TR of sequence in seconds.',
-                          default=1)
+                          default=0)
     optional.add_argument('-thr', '--threshold',
                           dest='thr',
                           type=float,

From 9f4ea24436daa292d04a0591f265ed05218cd025 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 20:00:33 +0100
Subject: [PATCH 14/42] removed unnecessary steps and corrected export error

---
 phys2bids/interfaces/acq.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/phys2bids/interfaces/acq.py b/phys2bids/interfaces/acq.py
index f6f358de8..97405408c 100644
--- a/phys2bids/interfaces/acq.py
+++ b/phys2bids/interfaces/acq.py
@@ -6,20 +6,20 @@
 """
 from bioread import read_file
 
-from phys2bids.physio_obj import blueprint_input, blueprint_output
+from phys2bids.physio_obj import blueprint_input
 
 
 def populate_phys_input(filename, chtrig):
     """
     Populate object phys_input
-    """        
+    """
 
     data = read_file(filename).channels
-    
+
     freq = [data[chtrig].samples_per_second] * 2
     timeseries = [data[chtrig].time_index, data[chtrig].data]
     units = ['s', data[chtrig].units]
-    names = ['time','trigger']
+    names = ['time', 'trigger']
 
     k = 0
     for ch in data:
@@ -30,4 +30,4 @@ def populate_phys_input(filename, chtrig):
             units.append(ch.units)
         k += 1
 
-    return phys_input = blueprint_input(timeseries, freq, names, units)
+    return blueprint_input(timeseries, freq, names, units)

From 6bb89fae22480ca866024ea5b03182d25b7410f5 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 20:05:09 +0100
Subject: [PATCH 15/42] Changed function has_data_size into has_size, added
 ch_amount to objects, added method to find offset in time in blueprint_input.

---
 phys2bids/physio_obj.py | 87 ++++++++++++++++++++++++++++-------------
 1 file changed, 60 insertions(+), 27 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index f661a1fe2..66f487dcf 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -5,10 +5,10 @@
 I/O objects for phys2bids.
 """
 
-from numpy import ndarray, shape
+import numpy as np
 
 
-def is_valid(var, type, list_type=None, return_var=True):
+def is_valid(var, var_type, list_type=None, return_var=True):
     """
     Checks that the var is of a certain type.
     If type is list and list_type is specified,
@@ -17,7 +17,7 @@ def is_valid(var, type, list_type=None, return_var=True):
     -----
     var:
         Variable to be checked.
-    type: type
+    var_type: type
         Type the variable is assumed to be.
     list_type: type
         As type.
@@ -27,10 +27,10 @@ def is_valid(var, type, list_type=None, return_var=True):
     var:
         Variable to be checked (same as input).
     """
-    if not isinstance(var, type):
-        raise AttributeError('Something went wrong while populating physio_io!')
+    if not isinstance(var, var_type):
+        raise AttributeError('Something went wrong while populating blueprint')
 
-    if type is list and list_type is not None:
+    if var_type is list and list_type is not None:
         for element in var:
             is_valid(element, list_type, return_var=False)
 
@@ -38,7 +38,7 @@ def is_valid(var, type, list_type=None, return_var=True):
         return var
 
 
-def has_data_size(var, data, token):
+def has_size(var, data_size, token):
     """
     Checks that the var has the same dimension of the data
     If it's not the case, fill in the var or removes exceding var entry.
@@ -46,8 +46,8 @@ def has_data_size(var, data, token):
     -----
     var:
         Variable to be checked.
-    data: (ch, [tps]) list or :obj:`numpy.ndarray`
-        Actual timeseries data.
+    data_size: int
+        Size of data of interest.
     token:
         What to be used in case of completion.
 
@@ -56,13 +56,6 @@ def has_data_size(var, data, token):
     var:
         Variable to be checked (same as input).
     """
-    if isinstance(data, list):
-        data_size = len(data)
-    elif isinstance(data, ndarray):
-        data_size = data.shape[0]
-    else:
-        raise Exception('Something went wrong assessing data size')
-
     if len(var) > data_size:
         var = var[:data_size]
 
@@ -80,7 +73,8 @@ class blueprint_input():
     Properties
     ----------
     timeseries : (ch, [tps]) list
-        List of numpy 1d arrays - one for channel.
+        List of numpy 1d arrays - one for channel, plus one for time.
+        Time channel has to be the first, trigger the second.
         Contains all the timeseries recorded.
         Supports different frequencies!
     freq : (ch, ) list
@@ -89,13 +83,51 @@ class blueprint_input():
         Support different frequencies!
     """
     def __init__(self, diff_timeseries, diff_freq, ch_name, units):
-        self.timeseries = is_valid(diff_timeseries, list, list_type=ndarray)
-        self.freq = has_data_size(is_valid(diff_freq, list,
+        self.timeseries = is_valid(diff_timeseries, list, list_type=np.ndarray)
+        self.ch_amount = len(self.timeseries)
+        self.freq = has_size(is_valid(diff_freq, list,
                                            list_type=(int, float)),
-                                  self.timeseries, 0)
-        self.ch_name = has_data_size(ch_name, self.timeseries, 'missing')
-        self.units = has_data_size(units, self.timeseries, '[]')
-        self.ch_num = len(self.timeseries)
+                                  self.ch_amount, 0)
+        self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
+        self.units = has_size(units, self.ch_amount, '[]')
+
+    def check_trigger_amount(self, thr=2.5, num_tps_expected=0, tr=0):
+        """
+
+        """
+        print('Counting trigger points')
+        trigger_deriv = np.diff(self.timeseries[1])
+        tps = trigger_deriv > thr
+        num_tps_found = tps.sum()
+        time_offset = self.timeseries[0][tps.argmax()]
+
+        if num_tps_expected:
+            print('Checking number of tps')
+            if num_tps_found > num_tps_expected:
+                tps_extra = num_tps_found - num_tps_expected
+                print(f'Found {tps_extra} tps more than expected!\n'
+                      'Assuming extra tps are at the end (try again with a '
+                      'more conservative thr)')
+
+            elif num_tps_found < num_tps_expected:
+                tps_missing = num_tps_expected - num_tps_found
+                print(f'Found {tps_missing} tps less than expected!')
+                if tr:
+                    print('Correcting time offset, assuming missing tps '
+                          'are at the beginning (try again with '
+                          'a more liberal thr')
+                    time_offset -= (tps_missing * tr)
+                else:
+                    print('Can\'t correct time offset, (try again specifying '
+                          'tr or with a more liberal thr')
+
+            else:
+                print('Found just the right amount of tps!')
+
+        else:
+            print('Cannot check the number of tps')
+
+        self.timeseries[0] -= time_offset
 
 
 class blueprint_output():
@@ -113,8 +145,9 @@ class blueprint_output():
         Shared frequency of the object.
     """
     def __init__(self, timeseries, freq, ch_name, units, start_time):
-        self.timeseries = is_valid(timeseries, ndarray)
-        self.freq = has_data_size(is_valid(freq, (int, float)), [1], 0)
-        self.ch_name = has_data_size(ch_name, self.timeseries, 'missing')
-        self.units = has_data_size(units, self.timeseries, '[]')
+        self.timeseries = is_valid(timeseries, np.ndarray)
+        self.ch_amount = self.timeseries.shape[0]
+        self.freq = has_size(is_valid(freq, (int, float)), 1, 0)
+        self.ch_name = has_size(ch_name, self.ch_amount, 'unkown')
+        self.units = has_size(units, self.ch_amount, '[]')
         self.start_time = start_time

From 600c0f9221b2f97574027b6220fa60a333bb8b38 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 20:06:17 +0100
Subject: [PATCH 16/42] Created new function to automatically detect extension
 of input file and check it's supported by phys2bids

---
 phys2bids/utils.py | 54 ++++++++++++++++++++++++++++++++++++----------
 1 file changed, 43 insertions(+), 11 deletions(-)

diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 937cebc46..8a85fe991 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -4,19 +4,49 @@
 import os
 import sys
 
+SUPPORTED_FTYPES = ('acq')  # , 'txt', 'mat', ...
+
 
 def check_input_dir(indir):
+    """
+    Checks that the given indir doesn't have a trailing '/'
+    """
     if indir[-1:] == '/':
         indir = indir[:-1]
 
     return indir
 
 
-def check_input_ext(file, ext):
-    if file[-len(ext):] != ext:
-        file = file + ext
+def check_input_ext(filename, ext):
+    """
+    Checks that the given file has the given extension
+    """
+    if filename[-len(ext):] != ext:
+        filename = filename + ext
 
-    return file
+    return filename
+
+
+def check_input_type(filename, indir):
+    """
+    Check which supported type is the filename.
+    Alternatively, raise an error if file not found or type not supported.
+    """
+    fftype_found = False
+    for ftype in SUPPORTED_FTYPES:
+        filename = check_input_ext(filename, ftype)
+        if os.path.isfile(os.path.join(indir, filename)):
+            fftype_found = True
+            break
+
+    if fftype_found:
+        print(f'File extension is .{ftype}')
+        return filename, ftype
+    else:
+        raise Exception(f'The file {filename} wasn\'t found in {indir}'
+                        f' or {ftype} is not supported yet.\n'
+                        f'phys2bids currently supports:'
+                        f' {", ".join(SUPPORTED_FTYPES)}')
 
 
 def path_exists_or_make_it(fldr):
@@ -27,12 +57,12 @@ def path_exists_or_make_it(fldr):
         os.makedirs(fldr)
 
 
-def check_file_exists(file, hardexit=True):
+def check_file_exists(filename):
     """
     Check if file exists.
     """
-    if not os.path.isfile(file) and file is not None:
-        raise FileNotFoundError(f'The file {file} does not exist!')
+    if not os.path.isfile(filename) and filename is not None:
+        raise FileNotFoundError(f'The file {filename} does not exist!')
 
 
 def print_info(filename, phys_object):
@@ -40,9 +70,10 @@ def print_info(filename, phys_object):
     Print the info of the input files, using blueprint_input object
     """
     print(f'File {filename} contains:\n')
-    
-    for ch in range(2, phys_object.ch_num):
-        print(f'{(ch-2):02d}. {phys_object.ch_name[ch]} sampled at {phys_object.freq[ch]} Hz')
+
+    for ch in range(2, phys_object.ch_amount):
+        print(f'{(ch-2):02d}. {phys_object.ch_name[ch]};'
+              f' sampled at {phys_object.freq[ch]} Hz')
 
 
 def move_file(oldpath, newpath, ext=''):
@@ -106,7 +137,8 @@ def load_heuristic(heuristic):
         from importlib import import_module
         try:
             mod = import_module(f'phys2bids.heuristics.{heuristic}')
-            mod.filename = mod.__file__.rstrip('co')  # remove c or o from pyc/pyo
+            # remove c or o from pyc/pyo
+            mod.filename = mod.__file__.rstrip('co')
         except Exception as exc:
             raise ImportError(f'Failed to import heuristic {heuristic}: {exc}')
     return mod

From be37a345a36d9ed8de1dc83c8b238f3ddd1df73b Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Fri, 22 Nov 2019 20:06:57 +0100
Subject: [PATCH 17/42] Started adjusting to new objects and functions.

---
 phys2bids/phys2bids.py | 64 ++++++++----------------------------------
 1 file changed, 11 insertions(+), 53 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 27b999568..52731dcce 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -26,7 +26,6 @@
 
 import os
 
-import numpy as np
 import pandas as pd
 
 from phys2bids import utils, viz
@@ -99,17 +98,10 @@ def _main(argv=None):
     options = _get_parser().parse_args(argv)
     # Check options to make them internally coherent
     # #!# This can probably be done while parsing?
-    # #!# Make filename check better somehow.
     options.indir = utils.check_input_dir(options.indir)
     options.outdir = utils.check_input_dir(options.outdir)
-    options.filename = utils.check_input_ext(options.filename, '.acq')
-    ftype = 'acq'
-    if not os.path.isfile(os.path.join(options.indir, options.filename)):
-        options.filename = utils.check_input_ext(options.filename[:-4], '.txt')
-        ftype = 'txt'
-
-    # #!# Change this to cases of and better message
-    print(f'File extension is .{ftype}')
+    options.filename, ftype = utils.check_input_type(options.filename,
+                                                     options.indir)
 
     if options.heur_file:
         options.heur_file = utils.check_input_ext(options.heur_file, '.py')
@@ -117,16 +109,14 @@ def _main(argv=None):
     infile = os.path.join(options.indir, options.filename)
     outfile = os.path.join(options.outdir, os.path.basename(options.filename[:-4]))
 
-    utils.check_file_exists(infile)
-    print('File exists')
-
     # Read file!
     if ftype == 'acq':
         from phys2bids.interfaces.acq import populate_phys_input
     elif ftype == 'txt':
         raise Exception('txt not yet supported')
     else:
-        raise Exception('File type not yet supported')
+        raise Exception('This shouldn\'t happen, check out the last few'
+                        'lines of code')
 
     phys_input = populate_phys_input(infile, options.chtrig)
     utils.print_info(options.filename, phys_input)
@@ -144,49 +134,17 @@ def _main(argv=None):
                   f'Skipping BIDS formatting.')
 
         # #!# Get option of no trigger! (which is wrong practice or Respiract)
-
-        # #!# MOVE THIS TO OBJECT METHOD! FROM HERE 
-        print('Counting trigger points')
-        trigger_deriv = np.diff(trigger)
-        tps = trigger_deriv > options.thr
-        num_tps_found = tps.sum()
-        time_offset = time[tps.argmax()]
-
-        if options.num_tps_expected:
-            print('Checking number of tps')
-            if num_tps_found > options.num_tps_expected:
-                tps_extra = num_tps_found - options.num_tps_expected
-                print('Found ' + str(tps_extra) + ' tps more than expected!\n',
-                      'Assuming extra tps are at the end (try again with a ',
-                      'more conservative thr)')
-            elif num_tps_found < options.num_tps_expected:
-                tps_missing = options.num_tps_expected - num_tps_found
-                print('Found ' + str(tps_missing) + ' tps less than expected!')
-                if options.tr:
-                    print('Correcting time offset, assuming missing tps'
-                          'are at the beginning')
-                    # time_offset = time_offset - (tps_missing * options.tr)
-                    time_offset = time[tps.argmax()] - (tps_missing * options.tr)
-                else:
-                    print('Can\'t correct time offset, (try again specifying',
-                          'tr or with a more liberal thr')
-
-            else:
-                print('Found just the right amount of tps!')
-
-        else:
-            print('Not checking the number of tps')
-
-        time = time - time_offset
-        # time = data[options.chtrig].time_index - time_offset
-
-        # #!# TO HERE
+        phys_input.check_trigger_amount(options.thr, options.num_tps_expected,
+                                        options.tr)
 
         utils.path_exists_or_make_it(options.outdir)
 
-        viz.plot_trigger(time, trigger, outfile, options)
+        viz.plot_trigger(phys_input.timeseries[0], phys_input.timeseries[1],
+                         outfile, options)
 
-        # #!# The following few lines could be a function on its own for use in python
+        #####
+        ###
+        # #!# This part has to become the "output object" population
         table = pd.DataFrame(index=time)
 
         if ftype == 'txt':

From 07f4245ae33415eb5e88ed03d8a9d42763c5e0f9 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 12:55:32 +0100
Subject: [PATCH 18/42] Pseudo code and docstrings

---
 phys2bids/phys2bids.py  |  6 ++++++
 phys2bids/physio_obj.py | 31 ++++++++++++++++++++++++++-----
 2 files changed, 32 insertions(+), 5 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 52731dcce..669d784a0 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -145,6 +145,12 @@ def _main(argv=None):
         #####
         ###
         # #!# This part has to become the "output object" population
+
+        # Check how many different frequencies there are in the input
+        # Create a dictionary that has one entry per frequence
+        # Create an output object per entry
+
+
         table = pd.DataFrame(index=time)
 
         if ftype == 'txt':
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 66f487dcf..830812401 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -72,28 +72,49 @@ class blueprint_input():
 
     Properties
     ----------
-    timeseries : (ch, [tps]) list
+    diff_timeseries : (ch, [tps]) list
         List of numpy 1d arrays - one for channel, plus one for time.
         Time channel has to be the first, trigger the second.
         Contains all the timeseries recorded.
         Supports different frequencies!
-    freq : (ch, ) list
+    diff_freq : (ch) list of floats
         List of floats - one per channel.
         Contains all the frequencies of the recorded channel.
         Support different frequencies!
+    ch_name : (ch) list of strings
+        List of names of the channels - can be the header of the columns
+        in the output files.
+    units : (ch) list of strings
+        List of the units of the channels.
+
+    Methods
+    -------
+    check_trigger_amount :
+        Method that counts the amounts of triggers and corrects time offset.
+
     """
     def __init__(self, diff_timeseries, diff_freq, ch_name, units):
         self.timeseries = is_valid(diff_timeseries, list, list_type=np.ndarray)
         self.ch_amount = len(self.timeseries)
         self.freq = has_size(is_valid(diff_freq, list,
-                                           list_type=(int, float)),
-                                  self.ch_amount, 0)
+                                      list_type=(int, float)),
+                             self.ch_amount, 0)
         self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')
 
     def check_trigger_amount(self, thr=2.5, num_tps_expected=0, tr=0):
         """
-
+        Method that counts trigger points and corrects time offset.
+
+        Input
+        -----
+        thr: float
+            threshold to be used to detect trigger points.
+            Default is 2.5
+        num_tps_expected: int
+            number of expected triggers (num of TRs in fMRI)
+        tr: float
+            the Repetition Time of the fMRI data.
         """
         print('Counting trigger points')
         trigger_deriv = np.diff(self.timeseries[1])

From 294e1225b4719f119a5002c8e3d9ebab48177545 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 13:41:05 +0100
Subject: [PATCH 19/42] Completed docstrings

---
 phys2bids/physio_obj.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 830812401..785ce1197 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -164,6 +164,16 @@ class blueprint_output():
         Impose same frequency!
     freq : float
         Shared frequency of the object.
+            Properties
+    ch_name : (ch) list of strings
+        List of names of the channels - can be the header of the columns
+        in the output files.
+    units : (ch) list of strings
+        List of the units of the channels.
+    start_time : float
+        Starting time of acquisition (equivalent to first TR,
+        or to the opposite sign of the time offset).
+
     """
     def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.timeseries = is_valid(timeseries, np.ndarray)

From f4223db1ef57166f57babb8d0eb0fc144ff8ae09 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 17:25:20 +0100
Subject: [PATCH 20/42] Added blueprint output and method to populate it from
 blueprint input

---
 phys2bids/physio_obj.py | 78 ++++++++++++++++++++++++++++++++---------
 1 file changed, 62 insertions(+), 16 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 785ce1197..9603ce703 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -69,15 +69,17 @@ class blueprint_input():
     """
     Main input object for phys2bids.
     Contains the blueprint to be populated.
+    !!! Pay attention: there's rules on how to populate this object.
+    See below ("Attention") !!!
 
-    Properties
-    ----------
-    diff_timeseries : (ch, [tps]) list
+    Input (Properties)
+    ------------------
+    timeseries : (ch, [tps]) list
         List of numpy 1d arrays - one for channel, plus one for time.
         Time channel has to be the first, trigger the second.
         Contains all the timeseries recorded.
         Supports different frequencies!
-    diff_freq : (ch) list of floats
+    freq : (ch) list of floats
         List of floats - one per channel.
         Contains all the frequencies of the recorded channel.
         Support different frequencies!
@@ -87,24 +89,47 @@ class blueprint_input():
     units : (ch) list of strings
         List of the units of the channels.
 
+    Properties
+    ---------------------
+    ch_amount: int
+        Number of channels (ch).
+
     Methods
     -------
     check_trigger_amount :
-        Method that counts the amounts of triggers and corrects time offset.
-
+        Method that counts the amounts of triggers and corrects time offset
+        in "time" ndarray.
+
+    Attention
+    ---------
+    The timeseries (and as a consequence, all the other properties)
+    should start with an entry for time and an entry for trigger.
+    Both should have the same length - hence same sampling. Meaning:
+    - timeseries[0] → ndarray representing time
+    - timeseries[1] → ndarray representing trigger
+    - timeseries[0].shape == timeseries[1].shape
+
+    As a consequence:
+    - freq[0] == freq[1]
+    - ch_name[0] = 'time'
+    - ch_name[1] = 'trigger'
+    - units[0] = 's'
+    - Actual number of channels (ANC) +1 <= ch_amount <= ANC +2
     """
-    def __init__(self, diff_timeseries, diff_freq, ch_name, units):
-        self.timeseries = is_valid(diff_timeseries, list, list_type=np.ndarray)
+    def __init__(self, timeseries, freq, ch_name, units):
+        self.timeseries = is_valid(timeseries, list, list_type=np.ndarray)
         self.ch_amount = len(self.timeseries)
-        self.freq = has_size(is_valid(diff_freq, list,
+        self.freq = has_size(is_valid(freq, list,
                                       list_type=(int, float)),
                              self.ch_amount, 0)
         self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')
 
-    def check_trigger_amount(self, thr=2.5, num_tps_expected=0, tr=0):
+    @classmethod
+    def check_trigger_amount(cls, thr=2.5, num_tps_expected=0, tr=0):
         """
-        Method that counts trigger points and corrects time offset.
+        Method that counts trigger points and corrects time offset in
+        the list representing time.
 
         Input
         -----
@@ -117,10 +142,10 @@ def check_trigger_amount(self, thr=2.5, num_tps_expected=0, tr=0):
             the Repetition Time of the fMRI data.
         """
         print('Counting trigger points')
-        trigger_deriv = np.diff(self.timeseries[1])
+        trigger_deriv = np.diff(cls.timeseries[1])
         tps = trigger_deriv > thr
         num_tps_found = tps.sum()
-        time_offset = self.timeseries[0][tps.argmax()]
+        time_offset = cls.timeseries[0][tps.argmax()]
 
         if num_tps_expected:
             print('Checking number of tps')
@@ -148,7 +173,7 @@ def check_trigger_amount(self, thr=2.5, num_tps_expected=0, tr=0):
         else:
             print('Cannot check the number of tps')
 
-        self.timeseries[0] -= time_offset
+        cls.timeseries[0] -= time_offset
 
 
 class blueprint_output():
@@ -156,8 +181,8 @@ class blueprint_output():
     Main output object for phys2bids.
     Contains the blueprint to be exported.
 
-    Properties
-    ----------
+    Properties - Input
+    ------------------
     timeseries : (ch x tps) :obj:`numpy.ndarray`
         Numpy 2d array of timeseries
         Contains all the timeseries recorded.
@@ -174,6 +199,10 @@ class blueprint_output():
         Starting time of acquisition (equivalent to first TR,
         or to the opposite sign of the time offset).
 
+    Methods
+    -------
+    init_from_blueprint:
+        method to populate from input blueprint instead of init
     """
     def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.timeseries = is_valid(timeseries, np.ndarray)
@@ -182,3 +211,20 @@ def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.ch_name = has_size(ch_name, self.ch_amount, 'unkown')
         self.units = has_size(units, self.ch_amount, '[]')
         self.start_time = start_time
+
+    @classmethod
+    def init_from_blueprint(cls, blueprint):
+        """
+        Method to populate the output blueprint using blueprint_input.
+
+        Input
+        -----
+        blueprint: :obj: blueprint_input
+            the input blueprint object
+        """
+        timeseries = np.asarray(blueprint.timeseries)
+        freq = blueprint.freq[0]
+        ch_name = blueprint.ch_name
+        units = blueprint.units
+        start_time = timeseries[0, 0]
+        return cls(timeseries, freq, ch_name, units, start_time)

From 2d57c5a56e10bf30f86e4570e8da9c0101da44c5 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 21:09:56 +0100
Subject: [PATCH 21/42] added methods to delete an indexed element and to
 return an indexed element

---
 phys2bids/physio_obj.py | 38 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 36 insertions(+), 2 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 9603ce703..64abd8ddb 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -125,7 +125,24 @@ def __init__(self, timeseries, freq, ch_name, units):
         self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')
 
-    @classmethod
+    def return_index(cls, idx):
+        """
+        Method that returns all the proper list entry of the
+        properties of the object, given an index.
+        """
+        return (cls.timeseries[idx], cls.ch_amount, cls.freq[idx],
+                cls.ch_name[idx], cls.units[idx])
+
+    def delete_at_index(cls, idx):
+        """
+        Method that returns all the proper list entry of the
+        properties of the object, given an index.
+        """
+        del(cls.timeseries[idx])
+        del(cls.freq[idx])
+        del(cls.ch_name[idx])
+        del(cls.units[idx])
+
     def check_trigger_amount(cls, thr=2.5, num_tps_expected=0, tr=0):
         """
         Method that counts trigger points and corrects time offset in
@@ -207,11 +224,28 @@ class blueprint_output():
     def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.timeseries = is_valid(timeseries, np.ndarray)
         self.ch_amount = self.timeseries.shape[0]
-        self.freq = has_size(is_valid(freq, (int, float)), 1, 0)
+        self.freq = is_valid(freq, (int, float))
         self.ch_name = has_size(ch_name, self.ch_amount, 'unkown')
         self.units = has_size(units, self.ch_amount, '[]')
         self.start_time = start_time
 
+    def return_index(cls, idx):
+        """
+        Method that returns all the proper list entry of the
+        properties of the object, given an index.
+        """
+        return (cls.timeseries[idx], cls.ch_amount, cls.freq,
+                cls.ch_name[idx], cls.units[idx], cls.start_time)
+
+    def delete_at_index(cls, idx):
+        """
+        Method that returns all the proper list entry of the
+        properties of the object, given an index.
+        """
+        del(cls.timeseries[idx])
+        del(cls.ch_name[idx])
+        del(cls.units[idx])
+
     @classmethod
     def init_from_blueprint(cls, blueprint):
         """

From 11c689c46438a26e1fdd3590f97782e5490ff7e4 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 21:10:30 +0100
Subject: [PATCH 22/42] Added creation of one class property (number of tr
 found)

---
 phys2bids/physio_obj.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 64abd8ddb..370428b19 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -191,6 +191,7 @@ def check_trigger_amount(cls, thr=2.5, num_tps_expected=0, tr=0):
             print('Cannot check the number of tps')
 
         cls.timeseries[0] -= time_offset
+        cls.num_tps_found = num_tps_found
 
 
 class blueprint_output():

From 75e638729aadbc7897f2b0193da16abc412256a8 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 21:11:23 +0100
Subject: [PATCH 23/42] Changed heuristic to add "recording" label

---
 phys2bids/phys2bids.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 669d784a0..25fd644a0 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -86,7 +86,10 @@ def use_heuristic(heur_file, sub, ses, filename, outdir):
     heur = utils.load_heuristic(heur_file)
     name = heur.heur(filename[:-4], name)
 
-    heurpath = fldr + '/' + name + '_physio'
+    if record_label:
+        recording = f'_recording-{record_label}'
+
+    heurpath = fldr + '/' + name + recording + '_physio'
     # for ext in ['.tsv.gz', '.json', '.log']:
     #     move_file(outfile, heurpath, ext)
     os.chdir(cwd)

From fd3413ea59e5308b5c4f941f00cac0876948877f Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Mon, 25 Nov 2019 21:13:03 +0100
Subject: [PATCH 24/42] Adapted channel selection for new objects, added
 frequency splitting and output object population, started writing real
 output.

---
 phys2bids/phys2bids.py | 158 ++++++++++++++++++++---------------------
 1 file changed, 77 insertions(+), 81 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 25fd644a0..f69191920 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -26,10 +26,12 @@
 
 import os
 
-import pandas as pd
+from copy import deepcopy
+from numpy import savetxt
 
 from phys2bids import utils, viz
 from phys2bids.cli.run import _get_parser
+from phys2bids.physio_obj import blueprint_output
 
 
 # #!# This is hardcoded until we find a better solution
@@ -59,7 +61,7 @@ def print_json(filename, samp_freq, time_offset, table_header):
     utils.writejson(filename, summary, indent=4, sort_keys=False)
 
 
-def use_heuristic(heur_file, sub, ses, filename, outdir):
+def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     utils.check_file_exists(heur_file)
 
     if sub[:4] != 'sub-':
@@ -121,104 +123,98 @@ def _main(argv=None):
         raise Exception('This shouldn\'t happen, check out the last few'
                         'lines of code')
 
-    phys_input = populate_phys_input(infile, options.chtrig)
-    utils.print_info(options.filename, phys_input)
+    phys_in = populate_phys_input(infile, options.chtrig)
+    utils.print_info(options.filename, phys_in)
 
     # If file has to be processed, process it
     if not options.info:
+        # If possible, prepare bids renaming.
         if options.heur_file and options.sub:
             utils.check_file_exists(options.heur_file)
             print(f'Preparing BIDS output using {options.heur_file}')
             outfile = use_heuristic(options.heur_file, options.sub,
                                     options.ses, options.filename,
-                                    options.outdir)
+                                    options.outdir, )
         elif options.heur_file and not options.sub:
             print(f'While "-heur" was specified, option "-sub" was not.\n'
                   f'Skipping BIDS formatting.')
 
         # #!# Get option of no trigger! (which is wrong practice or Respiract)
-        phys_input.check_trigger_amount(options.thr, options.num_tps_expected,
-                                        options.tr)
+        phys_in.check_trigger_amount(options.thr, options.num_tps_expected,
+                                     options.tr)
 
         utils.path_exists_or_make_it(options.outdir)
 
-        viz.plot_trigger(phys_input.timeseries[0], phys_input.timeseries[1],
+        viz.plot_trigger(phys_in.timeseries[0], phys_in.timeseries[1],
                          outfile, options)
 
-        #####
-        ###
-        # #!# This part has to become the "output object" population
-
-        # Check how many different frequencies there are in the input
-        # Create a dictionary that has one entry per frequence
-        # Create an output object per entry
-
-
-        table = pd.DataFrame(index=time)
-
-        if ftype == 'txt':
-            col_names = header[1].split('\t')
-            col_names[-1] = col_names[-1][:-1]
-
+        # The next few lines remove the undesired channels from phys_in.
         if options.chsel:
-            print('Extracting desired channels')
-            for ch in options.chsel:
-                if ftype == 'acq':
-                    table[data[ch].name] = data[ch].data
-                elif ftype == 'txt':
-                    # preparing channel names from txt file
-                    table[col_names[ch + 1]] = data[:, ch + 1]
-
-        else:
-            # #!# Needs a check on different channel frequency!
-            print('Extracting all channels')
-            if ftype == 'acq':
-                for ch in range(0, len(data)):
-                    table[data[ch].name] = data[ch].data
-            elif ftype == 'txt':
-                for ch in range(0, (data.shape[1] - 1)):
-                    table[col_names[ch + 1]] = data[:, ch + 1]
-
-        print('Extracting minor informations')
-        if ftype == 'acq':
-            samp_freq = data[0].samples_per_second
-        elif ftype == 'txt':
-            freq_list = header[0].split('\t')
-            samp_freq = 1 / float(freq_list[-1][:-2])
-
-        table.index.names = ['time']
-        table_width = len(table.columns)
-
-        if options.table_header:
-            if 'time' in options.table_header:
-                ignored_headers = 1
-            else:
-                ignored_headers = 0
-
-            n_headers = len(options.table_header)
-            if table_width < n_headers - ignored_headers:
-                print(f'Too many table headers specified!\n'
-                      f'{options.table_header}\n'
-                      f'Ignoring the last '
-                      f'{n_headers - table_width - ignored_headers}')
-                options.table_header = options.table_header[:(table_width + ignored_headers)]
-            elif table_width > n_headers - ignored_headers:
-                missing_headers = n_headers - table_width - ignored_headers
-                print(f'Not enough table headers specified!\n'
-                      f'{options.table_header}\n'
-                      f'Tailing {missing_headers} headers')
-                for i in range(missing_headers):
-                    options.table_header.append(f'missing n.{i+1}')
-
-            table.columns = options.table_header[ignored_headers:]
-            # #!# Here the function viz.plot_channel should be called for the desired channels.
-
-        print('Printing file')
-        table.to_csv(outfile + '.tsv.gz', sep='\t', index=True, header=False, compression='gzip')
-        # #!# Definitely needs check on samp_freq!
-        print_json(outfile, samp_freq, time_offset, options.table_header)
-        print_summary(options.filename, options.num_tps_expected,
-                      num_tps_found, samp_freq, time_offset, outfile)
+            for i in [x for x in reversed(range(0, phys_in.ch_amount))
+                      if x not in options.chsel]:
+                phys_in.delete_at_index(i)
+
+        # The next few lines create a dictionary of different blueprint_input
+        # objects, one for each unique frequency in phys_in
+        uniq_freq_list = set(phys_in.freq)
+        phys_out = {}
+        for uniq_freq in uniq_freq_list:
+            phys_out[uniq_freq] = deepcopy(phys_in)
+            for i in [i for i, x in enumerate(reversed(phys_in.freq))
+                      if x != uniq_freq]:
+                phys_out[uniq_freq].delete_at_index(phys_in.ch_amount-i-1)
+
+        for uniq_freq in uniq_freq_list:
+            phys_out[uniq_freq] = blueprint_output.init_from_blueprint(phys_out[uniq_freq])
+
+        # ####
+        # ###  This is to change channel names by manual input.
+        # #    It definitely needs to go before!
+        #
+        # if options.table_header:
+        #     if 'time' in options.table_header:
+        #         ignored_headers = 1
+        #     else:
+        #         ignored_headers = 0
+
+        #     n_headers = len(options.table_header)
+        #     if table_width < n_headers - ignored_headers:
+        #         print(f'Too many table headers specified!\n'
+        #               f'{options.table_header}\n'
+        #               f'Ignoring the last '
+        #               f'{n_headers - table_width - ignored_headers}')
+        #         options.table_header = options.table_header[:(table_width +
+        #                                                       ignored_headers)]
+        #     elif table_width > n_headers - ignored_headers:
+        #         missing_headers = n_headers - table_width - ignored_headers
+        #         print(f'Not enough table headers specified!\n'
+        #               f'{options.table_header}\n'
+        #               f'Tailing {missing_headers} headers')
+        #         for i in range(missing_headers):
+        #             options.table_header.append(f'missing n.{i+1}')
+
+        #     table.columns = options.table_header[ignored_headers:]
+            # #!# Here the function viz.plot_channel should be called
+            # for the desired channels.
+
+        output_amount = len(uniq_freq_list)
+        if output_amount > 1:
+            print(f'Found {output_amount} different frequencies in input!\n'
+                  f'Consequently, preparing {output_amount} of output files')
+
+        for uniq_freq in uniq_freq_list:
+            # ###
+            # ## Needs dealing with names
+            print('Printing file')
+            savetxt(outfile + '.tsv.gz', phys_out[uniq_freq].timeseries,
+                    fmt='%.8e', delimiter='\t')
+            print_json(outfile, phys_out[uniq_freq].freq,
+                       phys_out[uniq_freq].start_time,
+                       phys_out[uniq_freq].ch_name)
+            print_summary(options.filename, options.num_tps_expected,
+                          phys_out[uniq_freq].num_tps_found,
+                          phys_in.freq, phys_out[uniq_freq].start_time,
+                          outfile)
 
 
 if __name__ == '__main__':

From 4f806c030a7d2a5e893902ede32e3a8e59f8de9b Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 01:22:58 +0100
Subject: [PATCH 25/42] Renamed parser argument and changed default

---
 phys2bids/cli/run.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/phys2bids/cli/run.py b/phys2bids/cli/run.py
index 803083315..101d84a5d 100644
--- a/phys2bids/cli/run.py
+++ b/phys2bids/cli/run.py
@@ -95,14 +95,12 @@ def _get_parser():
                           type=float,
                           help='Threshold used for trigger detection.',
                           default=2.5)
-    optional.add_argument('-tbhd', '--table-header',
-                          dest='table_header',
+    optional.add_argument('-chnames', '--channel-names',
+                          dest='ch_name',
                           nargs='*',
                           type=str,
                           help='Columns header (for json file).',
-                          # #!# Has to go to empty list
-                          default=['time', 'respiratory_chest', 'trigger',
-                                   'cardiac', 'respiratory_CO2', 'respiratory_O2'])
+                          default=[''])
 
     optional.add_argument('-v', '--version', action='version',
                           version=('%(prog)s ' + __version__))

From 28e0406ed39005f069d4cf3c19b2b0dd85bee2ab Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 01:23:33 +0100
Subject: [PATCH 26/42] Improved docstrings, added method to rename channels in
 blueprint_input

---
 phys2bids/physio_obj.py | 82 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 69 insertions(+), 13 deletions(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 370428b19..cf151af5c 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -96,9 +96,15 @@ class blueprint_input():
 
     Methods
     -------
-    check_trigger_amount :
-        Method that counts the amounts of triggers and corrects time offset
-        in "time" ndarray.
+    return_index:
+        Returns the proper list entry of all the
+        properties of the object, given an index.
+    delete_at_index:
+        Returns all the proper list entry of the
+        properties of the object, given an index.
+    check_trigger_amount:
+        Counts the amounts of triggers and corrects time offset
+        in "time" ndarray. Also adds property ch_amount.
 
     Attention
     ---------
@@ -125,19 +131,53 @@ def __init__(self, timeseries, freq, ch_name, units):
         self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')
 
+    def rename_channels(cls, new_names, ch_trigger=None):
+        """
+        Renames the channels.
+
+        Input
+        -----
+        new_names: list of str
+            New names for channels.
+        ch_trigger:
+            Number of the channel containing the trigger.
+        """
+        if 'time' in new_names:
+            del(new_names[new_names.index['time']])
+
+        if 'trigger' in new_names:
+            del(new_names[new_names.index['trigger']])
+        elif ch_trigger:
+            del(new_names[ch_trigger])
+
+        new_names = ['time', 'trigger'] + new_names
+
+        cls.ch_name = has_size(is_valid(new_names, list, list_type=str),
+                               cls.ch_amount, 'unknown')
+
     def return_index(cls, idx):
         """
-        Method that returns all the proper list entry of the
+        Returns the proper list entry of all the
         properties of the object, given an index.
+
+        Input
+        -----
+        idx: int
+            Index of elements to return
         """
         return (cls.timeseries[idx], cls.ch_amount, cls.freq[idx],
                 cls.ch_name[idx], cls.units[idx])
 
     def delete_at_index(cls, idx):
         """
-        Method that returns all the proper list entry of the
+        Returns all the proper list entry of the
         properties of the object, given an index.
-        """
+
+        Input
+        -----
+        idx: int or range
+            Index of elements to delete from all lists
+         """
         del(cls.timeseries[idx])
         del(cls.freq[idx])
         del(cls.ch_name[idx])
@@ -145,18 +185,18 @@ def delete_at_index(cls, idx):
 
     def check_trigger_amount(cls, thr=2.5, num_tps_expected=0, tr=0):
         """
-        Method that counts trigger points and corrects time offset in
+        Counts trigger points and corrects time offset in
         the list representing time.
 
         Input
         -----
         thr: float
-            threshold to be used to detect trigger points.
+            Threshold to be used to detect trigger points.
             Default is 2.5
         num_tps_expected: int
-            number of expected triggers (num of TRs in fMRI)
+            Number of expected triggers (num of TRs in fMRI)
         tr: float
-            the Repetition Time of the fMRI data.
+            The Repetition Time of the fMRI data.
         """
         print('Counting trigger points')
         trigger_deriv = np.diff(cls.timeseries[1])
@@ -219,6 +259,12 @@ class blueprint_output():
 
     Methods
     -------
+    return_index:
+        Returns the proper list entry of all the
+        properties of the object, given an index.
+    delete_at_index:
+        Returns all the proper list entry of the
+        properties of the object, given an index.
     init_from_blueprint:
         method to populate from input blueprint instead of init
     """
@@ -232,16 +278,26 @@ def __init__(self, timeseries, freq, ch_name, units, start_time):
 
     def return_index(cls, idx):
         """
-        Method that returns all the proper list entry of the
+        Returns all the proper list entry of the
         properties of the object, given an index.
+
+        Input
+        -----
+        idx: int
+            Index of elements to return
         """
         return (cls.timeseries[idx], cls.ch_amount, cls.freq,
                 cls.ch_name[idx], cls.units[idx], cls.start_time)
 
     def delete_at_index(cls, idx):
         """
-        Method that returns all the proper list entry of the
+        Returns all the proper list entry of the
         properties of the object, given an index.
+
+        Input
+        -----
+        idx: int or range
+            Index of elements to delete from all lists
         """
         del(cls.timeseries[idx])
         del(cls.ch_name[idx])
@@ -255,7 +311,7 @@ def init_from_blueprint(cls, blueprint):
         Input
         -----
         blueprint: :obj: blueprint_input
-            the input blueprint object
+            The input blueprint object
         """
         timeseries = np.asarray(blueprint.timeseries)
         freq = blueprint.freq[0]

From cfc333e7d85666aeec25b58a6983b506221ecd78 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 01:27:10 +0100
Subject: [PATCH 27/42] renamed "table_header" into "ch_name", added a check on
 input file existence, moved heuristics around, added renaming of channels
 using new classes, improved bids naming and output in case of multiple
 frequencies.

---
 phys2bids/phys2bids.py | 94 +++++++++++++++++++-----------------------
 1 file changed, 43 insertions(+), 51 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index f69191920..4fc72c267 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -53,11 +53,11 @@ def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, out
     utils.writefile(outfile, '.log', summary)
 
 
-def print_json(filename, samp_freq, time_offset, table_header):
+def print_json(filename, samp_freq, time_offset, ch_name):
     start_time = -time_offset
     summary = dict(SamplingFrequency=samp_freq,
                    StartTime=start_time,
-                   Columns=table_header)
+                   Columns=ch_name)
     utils.writejson(filename, summary, indent=4, sort_keys=False)
 
 
@@ -110,8 +110,10 @@ def _main(argv=None):
 
     if options.heur_file:
         options.heur_file = utils.check_input_ext(options.heur_file, '.py')
+        utils.check_file_exists(options.heur_file)
 
     infile = os.path.join(options.indir, options.filename)
+    utils.check_file_exists(infile)
     outfile = os.path.join(options.outdir, os.path.basename(options.filename[:-4]))
 
     # Read file!
@@ -120,43 +122,44 @@ def _main(argv=None):
     elif ftype == 'txt':
         raise Exception('txt not yet supported')
     else:
-        raise Exception('This shouldn\'t happen, check out the last few'
+        raise Exception('This shouldn\'t happen, check out the last few '
                         'lines of code')
 
+    print('Reading the file')
     phys_in = populate_phys_input(infile, options.chtrig)
+    print('Reading infos')
     utils.print_info(options.filename, phys_in)
+    # #!# Here the function viz.plot_channel should be called
+    # for the desired channels.
 
     # If file has to be processed, process it
     if not options.info:
-        # If possible, prepare bids renaming.
-        if options.heur_file and options.sub:
-            utils.check_file_exists(options.heur_file)
-            print(f'Preparing BIDS output using {options.heur_file}')
-            outfile = use_heuristic(options.heur_file, options.sub,
-                                    options.ses, options.filename,
-                                    options.outdir, )
-        elif options.heur_file and not options.sub:
-            print(f'While "-heur" was specified, option "-sub" was not.\n'
-                  f'Skipping BIDS formatting.')
 
         # #!# Get option of no trigger! (which is wrong practice or Respiract)
         phys_in.check_trigger_amount(options.thr, options.num_tps_expected,
                                      options.tr)
-
+        print('Checking that the output folder exists')
         utils.path_exists_or_make_it(options.outdir)
-
+        print('Plot trigger')
         viz.plot_trigger(phys_in.timeseries[0], phys_in.timeseries[1],
                          outfile, options)
 
         # The next few lines remove the undesired channels from phys_in.
         if options.chsel:
+            print('Dropping unselected channels')
             for i in [x for x in reversed(range(0, phys_in.ch_amount))
                       if x not in options.chsel]:
                 phys_in.delete_at_index(i)
 
+        # If requested, change channel names.
+        if options.ch_name:
+            print('Renaming channels with given names')
+            phys_in.rename_channels(options.ch_name)
+
         # The next few lines create a dictionary of different blueprint_input
         # objects, one for each unique frequency in phys_in
         uniq_freq_list = set(phys_in.freq)
+        print(f'Found {len(uniq_freq_list)} unique frequencies.')
         phys_out = {}
         for uniq_freq in uniq_freq_list:
             phys_out[uniq_freq] = deepcopy(phys_in)
@@ -167,54 +170,43 @@ def _main(argv=None):
         for uniq_freq in uniq_freq_list:
             phys_out[uniq_freq] = blueprint_output.init_from_blueprint(phys_out[uniq_freq])
 
-        # ####
-        # ###  This is to change channel names by manual input.
-        # #    It definitely needs to go before!
-        #
-        # if options.table_header:
-        #     if 'time' in options.table_header:
-        #         ignored_headers = 1
-        #     else:
-        #         ignored_headers = 0
-
-        #     n_headers = len(options.table_header)
-        #     if table_width < n_headers - ignored_headers:
-        #         print(f'Too many table headers specified!\n'
-        #               f'{options.table_header}\n'
-        #               f'Ignoring the last '
-        #               f'{n_headers - table_width - ignored_headers}')
-        #         options.table_header = options.table_header[:(table_width +
-        #                                                       ignored_headers)]
-        #     elif table_width > n_headers - ignored_headers:
-        #         missing_headers = n_headers - table_width - ignored_headers
-        #         print(f'Not enough table headers specified!\n'
-        #               f'{options.table_header}\n'
-        #               f'Tailing {missing_headers} headers')
-        #         for i in range(missing_headers):
-        #             options.table_header.append(f'missing n.{i+1}')
-
-        #     table.columns = options.table_header[ignored_headers:]
-            # #!# Here the function viz.plot_channel should be called
-            # for the desired channels.
-
         output_amount = len(uniq_freq_list)
         if output_amount > 1:
             print(f'Found {output_amount} different frequencies in input!\n'
                   f'Consequently, preparing {output_amount} of output files')
 
+        if options.heur_file and options.sub:
+            print(f'Preparing BIDS output using {options.heur_file}')
+        elif options.heur_file and not options.sub:
+            print(f'While "-heur" was specified, option "-sub" was not.\n'
+                  f'Skipping BIDS formatting.')
+
         for uniq_freq in uniq_freq_list:
-            # ###
-            # ## Needs dealing with names
-            print('Printing file')
+            # If possible, prepare bids renaming.
+            if options.heur_file and options.sub:
+                if output_amount > 1:
+                    # Add "recording-freq" to filename if more than one freq
+                    outfile = use_heuristic(options.heur_file, options.sub,
+                                            options.ses, options.filename,
+                                            options.outdir, uniq_freq)
+                else:
+                    outfile = use_heuristic(options.heur_file, options.sub,
+                                            options.ses, options.filename,
+                                            options.outdir)
+
+            elif output_amount > 1:
+                # Append "freq" to filename if more than one freq
+                outfile = f'outfile_{uniq_freq}'
+
+            print('Exporting files for freq {uniq_freq}')
             savetxt(outfile + '.tsv.gz', phys_out[uniq_freq].timeseries,
                     fmt='%.8e', delimiter='\t')
             print_json(outfile, phys_out[uniq_freq].freq,
                        phys_out[uniq_freq].start_time,
                        phys_out[uniq_freq].ch_name)
             print_summary(options.filename, options.num_tps_expected,
-                          phys_out[uniq_freq].num_tps_found,
-                          phys_in.freq, phys_out[uniq_freq].start_time,
-                          outfile)
+                          phys_in.num_tps_found, uniq_freq,
+                          phys_out[uniq_freq].start_time, outfile)
 
 
 if __name__ == '__main__':

From 2c61fa15eaa7c1fc3414b794dfa47461ea00ca0c Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 13:35:52 +0100
Subject: [PATCH 28/42] Addressed @eurunuela 's review to PR #38

---
 phys2bids/phys2bids.py  |  18 +++----
 phys2bids/physio_obj.py | 111 +++++++++++++++++++++++++++++-----------
 2 files changed, 89 insertions(+), 40 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 4fc72c267..93e2538c4 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -122,8 +122,8 @@ def _main(argv=None):
     elif ftype == 'txt':
         raise Exception('txt not yet supported')
     else:
-        raise Exception('This shouldn\'t happen, check out the last few '
-                        'lines of code')
+        # #!# We should add a logger here.
+        raise Exception('Currently unsupported file type.')
 
     print('Reading the file')
     phys_in = populate_phys_input(infile, options.chtrig)
@@ -147,9 +147,9 @@ def _main(argv=None):
         # The next few lines remove the undesired channels from phys_in.
         if options.chsel:
             print('Dropping unselected channels')
-            for i in [x for x in reversed(range(0, phys_in.ch_amount))
-                      if x not in options.chsel]:
-                phys_in.delete_at_index(i)
+            for i in reversed(range(0, phys_in.ch_amout)):
+                if i not in options.chsel:
+                    phys_in.delete_at_index(i)
 
         # If requested, change channel names.
         if options.ch_name:
@@ -163,9 +163,9 @@ def _main(argv=None):
         phys_out = {}
         for uniq_freq in uniq_freq_list:
             phys_out[uniq_freq] = deepcopy(phys_in)
-            for i in [i for i, x in enumerate(reversed(phys_in.freq))
-                      if x != uniq_freq]:
-                phys_out[uniq_freq].delete_at_index(phys_in.ch_amount-i-1)
+            for i in reversed(phys_in.freq):
+                if i != uniq_freq:
+                    phys_out[uniq_freq].delete_at_index(phys_in.ch_amount-i-1)
 
         for uniq_freq in uniq_freq_list:
             phys_out[uniq_freq] = blueprint_output.init_from_blueprint(phys_out[uniq_freq])
@@ -173,7 +173,7 @@ def _main(argv=None):
         output_amount = len(uniq_freq_list)
         if output_amount > 1:
             print(f'Found {output_amount} different frequencies in input!\n'
-                  f'Consequently, preparing {output_amount} of output files')
+                  f'Preparing {output_amount} output files')
 
         if options.heur_file and options.sub:
             print(f'Preparing BIDS output using {options.heur_file}')
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index cf151af5c..c1cb324da 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -20,7 +20,10 @@ def is_valid(var, var_type, list_type=None, return_var=True):
     var_type: type
         Type the variable is assumed to be.
     list_type: type
-        As type.
+        Like var_type, but applies to list elements.
+    return_var: boolean
+        If true, the function returns the input variable.
+        Useful for checking over assignment.
 
     Output
     ------
@@ -28,7 +31,7 @@ def is_valid(var, var_type, list_type=None, return_var=True):
         Variable to be checked (same as input).
     """
     if not isinstance(var, var_type):
-        raise AttributeError('Something went wrong while populating blueprint')
+        raise AttributeError(f'The given variable is not a {var_type}')
 
     if var_type is list and list_type is not None:
         for element in var:
@@ -44,12 +47,14 @@ def has_size(var, data_size, token):
     If it's not the case, fill in the var or removes exceding var entry.
     Input
     -----
-    var:
+    var: any type
         Variable to be checked.
     data_size: int
         Size of data of interest.
-    token:
-        What to be used in case of completion.
+    token: same type as `var`
+        If `var` doesn't have as many elements as the data_size,
+        it will be padded at the end with this `token`.
+        It has to be the same type as var.
 
     Output
     ------
@@ -60,6 +65,7 @@ def has_size(var, data_size, token):
         var = var[:data_size]
 
     if len(var) < data_size:
+        is_valid(token, type(var))
         var = var + [token] * (data_size - len(var))
 
     return var
@@ -90,12 +96,20 @@ class blueprint_input():
         List of the units of the channels.
 
     Properties
-    ---------------------
+    ----------
     ch_amount: int
         Number of channels (ch).
 
+    Optional properties
+    -------------------
+    num_timepoints_found: int
+        Amount of timepoints found in the automatic count,
+        *if* check_trigger_amount() is run
+
     Methods
     -------
+    rename_channels:
+        Changes the list "ch_name" in a controlled way.
     return_index:
         Returns the proper list entry of all the
         properties of the object, given an index.
@@ -137,6 +151,8 @@ def rename_channels(cls, new_names, ch_trigger=None):
 
         Input
         -----
+        cls: :obj: `blueprint_input`
+            The object on which to operate
         new_names: list of str
             New names for channels.
         ch_trigger:
@@ -162,8 +178,16 @@ def return_index(cls, idx):
 
         Input
         -----
+        cls: :obj: `blueprint_input`
+            The object on which to operate
         idx: int
             Index of elements to return
+
+        Output
+        ------
+        out: tuple
+            Tuple containing the proper list entry of all the
+            properties of the object with index `idx`
         """
         return (cls.timeseries[idx], cls.ch_amount, cls.freq[idx],
                 cls.ch_name[idx], cls.units[idx])
@@ -175,6 +199,8 @@ def delete_at_index(cls, idx):
 
         Input
         -----
+        cls: :obj: `blueprint_input`
+            The object on which to operate
         idx: int or range
             Index of elements to delete from all lists
          """
@@ -183,55 +209,61 @@ def delete_at_index(cls, idx):
         del(cls.ch_name[idx])
         del(cls.units[idx])
 
-    def check_trigger_amount(cls, thr=2.5, num_tps_expected=0, tr=0):
+    def check_trigger_amount(cls, thr=2.5, num_timepoints_expected=0, tr=0):
         """
         Counts trigger points and corrects time offset in
         the list representing time.
 
         Input
         -----
+        cls: :obj: `blueprint_input`
+            The object on which to operate
         thr: float
             Threshold to be used to detect trigger points.
             Default is 2.5
-        num_tps_expected: int
+        num_timepoints_expected: int
             Number of expected triggers (num of TRs in fMRI)
         tr: float
             The Repetition Time of the fMRI data.
         """
         print('Counting trigger points')
         trigger_deriv = np.diff(cls.timeseries[1])
-        tps = trigger_deriv > thr
-        num_tps_found = tps.sum()
-        time_offset = cls.timeseries[0][tps.argmax()]
-
-        if num_tps_expected:
-            print('Checking number of tps')
-            if num_tps_found > num_tps_expected:
-                tps_extra = num_tps_found - num_tps_expected
-                print(f'Found {tps_extra} tps more than expected!\n'
-                      'Assuming extra tps are at the end (try again with a '
-                      'more conservative thr)')
-
-            elif num_tps_found < num_tps_expected:
-                tps_missing = num_tps_expected - num_tps_found
-                print(f'Found {tps_missing} tps less than expected!')
+        timepoints = trigger_deriv > thr
+        num_timepoints_found = timepoints.sum()
+        time_offset = cls.timeseries[0][timepoints.argmax()]
+
+        if num_timepoints_expected:
+            print('Checking number of timepoints')
+            if num_timepoints_found > num_timepoints_expected:
+                timepoints_extra = (num_timepoints_found -
+                                    num_timepoints_expected)
+                print(f'Found {timepoints_extra} timepoints'
+                      'more than expected!\n'
+                      'Assuming extra timepoints are at the end '
+                      '(try again with a more conservative thr)')
+
+            elif num_timepoints_found < num_timepoints_expected:
+                timepoints_missing = (num_timepoints_expected -
+                                      num_timepoints_found)
+                print(f'Found {timepoints_missing} timepoints'
+                      'less than expected!')
                 if tr:
-                    print('Correcting time offset, assuming missing tps '
-                          'are at the beginning (try again with '
+                    print('Correcting time offset, assuming missing timepoints'
+                          ' are at the beginning (try again with '
                           'a more liberal thr')
-                    time_offset -= (tps_missing * tr)
+                    time_offset -= (timepoints_missing * tr)
                 else:
                     print('Can\'t correct time offset, (try again specifying '
                           'tr or with a more liberal thr')
 
             else:
-                print('Found just the right amount of tps!')
+                print('Found just the right amount of timepoints!')
 
         else:
-            print('Cannot check the number of tps')
+            print('Cannot check the number of timepoints')
 
         cls.timeseries[0] -= time_offset
-        cls.num_tps_found = num_tps_found
+        cls.num_timepoints_found = num_timepoints_found
 
 
 class blueprint_output():
@@ -272,7 +304,7 @@ def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.timeseries = is_valid(timeseries, np.ndarray)
         self.ch_amount = self.timeseries.shape[0]
         self.freq = is_valid(freq, (int, float))
-        self.ch_name = has_size(ch_name, self.ch_amount, 'unkown')
+        self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')
         self.start_time = start_time
 
@@ -283,8 +315,16 @@ def return_index(cls, idx):
 
         Input
         -----
+        cls: :obj: `blueprint_output`
+            The object on which to operate
         idx: int
             Index of elements to return
+
+        Output
+        ------
+        out: tuple
+            Tuple containing the proper list entry of all the
+            properties of the object with index `idx`
         """
         return (cls.timeseries[idx], cls.ch_amount, cls.freq,
                 cls.ch_name[idx], cls.units[idx], cls.start_time)
@@ -296,6 +336,8 @@ def delete_at_index(cls, idx):
 
         Input
         -----
+        cls: :obj: `blueprint_output`
+            The object on which to operate
         idx: int or range
             Index of elements to delete from all lists
         """
@@ -310,8 +352,15 @@ def init_from_blueprint(cls, blueprint):
 
         Input
         -----
-        blueprint: :obj: blueprint_input
+        cls: :obj: `blueprint_output`
+            The object on which to operate
+        blueprint: :obj: `blueprint_input`
             The input blueprint object
+
+        Output
+        ------
+        cls: :obj: `blueprint_output`
+            Populated `blueprint_output` object.
         """
         timeseries = np.asarray(blueprint.timeseries)
         freq = blueprint.freq[0]

From 9b139d6e776b98a97e2a79451c952a2a9333f03a Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 16:53:27 +0100
Subject: [PATCH 29/42] Added more docstrings, Keep addressing @eurunuela's
 review to PR #38, added heudiconv copyright and license

---
 phys2bids/phys2bids.py  | 86 ++++++++++++++++++++++++++++++++++++++++-
 phys2bids/physio_obj.py | 41 ++++++++++++++++++--
 phys2bids/utils.py      |  8 ++++
 3 files changed, 129 insertions(+), 6 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 93e2538c4..8f6a98527 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -39,6 +39,31 @@
 
 
 def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, outfile):
+    """
+    Prints a summary onscreen and in file with informations on the files.
+
+    Input
+    -----
+    filename: str
+        Name of the input of phys2bids.
+    ntp_expected: int
+        Number of expected timepoints, as defined by user.
+    ntp_found: int
+        Number of timepoints found with the automatic process.
+    samp_freq: float
+        Frequency of sampling for the output file.
+    time_offset: float
+        Difference between beginning of file and first TR.
+    outfile: str or path
+        Fullpath to output file.
+
+    Outcome
+    -------
+    summary: str
+        Prints the summary on screen
+    outfile: .log file
+        File containing summary
+    """
     start_time = -time_offset
     summary = (f'------------------------------------------------\n'
                f'Filename:            {filename}\n'
@@ -53,16 +78,61 @@ def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, out
     utils.writefile(outfile, '.log', summary)
 
 
-def print_json(filename, samp_freq, time_offset, ch_name):
+def print_json(outfile, samp_freq, time_offset, ch_name):
+    """
+    Prints the json required by BIDS format.
+
+    Input
+    -----
+    outfile: str or path
+        Fullpath to output file.
+    samp_freq: float
+        Frequency of sampling for the output file.
+    time_offset: float
+        Difference between beginning of file and first TR.
+    ch_name: list of str
+        List of channel names, as specified by BIDS format.
+
+    Outcome
+    -------
+
+    outfile: .json file
+        File containing information for BIDS.
+    """
     start_time = -time_offset
     summary = dict(SamplingFrequency=samp_freq,
                    StartTime=start_time,
                    Columns=ch_name)
-    utils.writejson(filename, summary, indent=4, sort_keys=False)
+    utils.writejson(outfile, summary, indent=4, sort_keys=False)
 
 
 def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     utils.check_file_exists(heur_file)
+    """
+    Import the heuristic file specified by the user and uses its output
+    to rename the file.
+
+    Input
+    -----
+    heur_file: str or path
+        Fullpath to heuristic file.
+    sub: str or int
+        Name of subject.
+    ses: str or int or None
+        Name of session.
+    filename: str
+        Name of the input of phys2bids.
+    outdir: str or path
+        Path to the directory that will become the "site" folder
+        ("root" folder of BIDS database).
+    record_label: str
+        Optional label for the "record" entry of BIDS.
+
+    Output
+    -------
+    heurpath: str or path
+        Returned fullpath to tsv.gz new file (post BIDS formatting).
+    """
 
     if sub[:4] != 'sub-':
         name = 'sub-' + sub
@@ -100,6 +170,15 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
 
 
 def _main(argv=None):
+    """
+    Main workflow of phys2bids.
+    Runs the parser, does some checks on input, then imports
+    the right interface file to read the input. If only info is required,
+    it returns a summary onscreen.
+    Otherwise, it operates on the input to return a .tsv.gz file, possibily
+    in BIDS format.
+
+    """
     options = _get_parser().parse_args(argv)
     # Check options to make them internally coherent
     # #!# This can probably be done while parsing?
@@ -167,6 +246,9 @@ def _main(argv=None):
                 if i != uniq_freq:
                     phys_out[uniq_freq].delete_at_index(phys_in.ch_amount-i-1)
 
+        # Create a blueprint_output object for each unique frequency found.
+        # Populate it with the corresponding blueprint input and replace it
+        # in the dictionary.
         for uniq_freq in uniq_freq_list:
             phys_out[uniq_freq] = blueprint_output.init_from_blueprint(phys_out[uniq_freq])
 
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index c1cb324da..9b0b6df0a 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -15,7 +15,7 @@ def is_valid(var, var_type, list_type=None, return_var=True):
     checks that the list contains list_type.
     Input
     -----
-    var:
+    var: any type
         Variable to be checked.
     var_type: type
         Type the variable is assumed to be.
@@ -27,7 +27,7 @@ def is_valid(var, var_type, list_type=None, return_var=True):
 
     Output
     ------
-    var:
+    var: any type
         Variable to be checked (same as input).
     """
     if not isinstance(var, var_type):
@@ -58,7 +58,7 @@ def has_size(var, data_size, token):
 
     Output
     ------
-    var:
+    var: any type
         Variable to be checked (same as input).
     """
     if len(var) > data_size:
@@ -147,7 +147,8 @@ def __init__(self, timeseries, freq, ch_name, units):
 
     def rename_channels(cls, new_names, ch_trigger=None):
         """
-        Renames the channels.
+        Renames the channels. If 'time' or 'trigger' were specified,
+        it makes sure that they're the first and second entry.
 
         Input
         -----
@@ -157,6 +158,11 @@ def rename_channels(cls, new_names, ch_trigger=None):
             New names for channels.
         ch_trigger:
             Number of the channel containing the trigger.
+
+        Outcome
+        -------
+        cls.ch_name:
+            Changes content to new_name.
         """
         if 'time' in new_names:
             del(new_names[new_names.index['time']])
@@ -203,6 +209,12 @@ def delete_at_index(cls, idx):
             The object on which to operate
         idx: int or range
             Index of elements to delete from all lists
+
+        Outcome
+        -------
+        cls:
+            In all the property that are lists, the element correspondent to
+            `idx` gets deleted
          """
         del(cls.timeseries[idx])
         del(cls.freq[idx])
@@ -225,8 +237,23 @@ def check_trigger_amount(cls, thr=2.5, num_timepoints_expected=0, tr=0):
             Number of expected triggers (num of TRs in fMRI)
         tr: float
             The Repetition Time of the fMRI data.
+
+        Output
+        ------
+        cls.num_timepoints_found: int
+            Property of the `blueprint_input` class.
+            Contains the number of timepoints found
+            with the automatic estimation.
+
+        Outcome
+        -------
+        cls.timeseries:
+            The property `timeseries` is shifted with the 0 being
+            the time of first trigger.
         """
         print('Counting trigger points')
+        # Use first derivative of the trigger channel to find the TRs,
+        # comparing it to a given threshold.
         trigger_deriv = np.diff(cls.timeseries[1])
         timepoints = trigger_deriv > thr
         num_timepoints_found = timepoints.sum()
@@ -340,6 +367,12 @@ def delete_at_index(cls, idx):
             The object on which to operate
         idx: int or range
             Index of elements to delete from all lists
+
+        Outcome
+        -------
+        cls:
+            In all the property that are lists, the element correspondent to
+            `idx` gets deleted
         """
         del(cls.timeseries[idx])
         del(cls.ch_name[idx])
diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 8a85fe991..905887df9 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -105,11 +105,18 @@ def copy_file(oldpath, newpath, ext=''):
 
 
 def writefile(filename, ext, text):
+    """
+    Produces a textfile of the specified extension `ext`,
+    containing the given content `text`
+    """
     with open(filename + ext, 'w') as text_file:
         print(text, file=text_file)
 
 
 def writejson(filename, data, **kwargs):
+    """
+    Outputs a json file with the given data inside.
+    """
     if not filename.endswith('.json'):
         filename += '.json'
     with open(filename, 'w') as out:
@@ -122,6 +129,7 @@ def load_heuristic(heuristic):
     References
     ----------
     Copied from [nipy/heudiconv](https://github.com/nipy/heudiconv)
+    Copyright [2014-2019] [Heudiconv developers], Apache 2 license.
     """
     if os.path.sep in heuristic or os.path.lexists(heuristic):
         heuristic_file = os.path.realpath(heuristic)

From c924c325bab30ecd7bca29a5c5106035903e3235 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 23:36:58 +0100
Subject: [PATCH 30/42] Addressed @rmarkello 's reviews in PR #38

---
 phys2bids/cli/run.py        |   4 +-
 phys2bids/interfaces/acq.py |   8 +-
 phys2bids/phys2bids.py      | 155 ++++++++++++++++++------------------
 phys2bids/physio_obj.py     | 101 ++++++++++++-----------
 phys2bids/utils.py          |  20 +++--
 5 files changed, 144 insertions(+), 144 deletions(-)

diff --git a/phys2bids/cli/run.py b/phys2bids/cli/run.py
index 101d84a5d..4edf18e54 100644
--- a/phys2bids/cli/run.py
+++ b/phys2bids/cli/run.py
@@ -73,7 +73,7 @@ def _get_parser():
                           type=int,
                           help=('The number corresponding to the trigger channel.'
                                 ' Channel numbering starts with 0'),
-                          default=1)
+                          default=0)
     optional.add_argument('-chsel', '--channel-selection',
                           dest='chsel',
                           nargs='*',
@@ -100,7 +100,7 @@ def _get_parser():
                           nargs='*',
                           type=str,
                           help='Columns header (for json file).',
-                          default=[''])
+                          default=None)
 
     optional.add_argument('-v', '--version', action='version',
                           version=('%(prog)s ' + __version__))
diff --git a/phys2bids/interfaces/acq.py b/phys2bids/interfaces/acq.py
index 97405408c..7ef73710e 100644
--- a/phys2bids/interfaces/acq.py
+++ b/phys2bids/interfaces/acq.py
@@ -6,7 +6,7 @@
 """
 from bioread import read_file
 
-from phys2bids.physio_obj import blueprint_input
+from phys2bids.physio_obj import BlueprintInput
 
 
 def populate_phys_input(filename, chtrig):
@@ -21,13 +21,11 @@ def populate_phys_input(filename, chtrig):
     units = ['s', data[chtrig].units]
     names = ['time', 'trigger']
 
-    k = 0
-    for ch in data:
+    for k, ch in enumerate(data):
         if k != chtrig:
             print(f'{k:02d}. {ch}')
             timeseries.append(ch.data)
             freq.append(ch.samples_per_second)
             units.append(ch.units)
-        k += 1
 
-    return blueprint_input(timeseries, freq, names, units)
+    return BlueprintInput(timeseries, freq, names, units)
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 8f6a98527..5667a818e 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -31,7 +31,7 @@
 
 from phys2bids import utils, viz
 from phys2bids.cli.run import _get_parser
-from phys2bids.physio_obj import blueprint_output
+from phys2bids.physio_obj import BlueprintOutput
 
 
 # #!# This is hardcoded until we find a better solution
@@ -193,16 +193,17 @@ def _main(argv=None):
 
     infile = os.path.join(options.indir, options.filename)
     utils.check_file_exists(infile)
-    outfile = os.path.join(options.outdir, os.path.basename(options.filename[:-4]))
+    outfile = os.path.join(options.outdir,
+                           os.path.basename(os.path.splitext(options.filename)))
 
     # Read file!
     if ftype == 'acq':
         from phys2bids.interfaces.acq import populate_phys_input
     elif ftype == 'txt':
-        raise Exception('txt not yet supported')
+        raise NotImplementedError('txt not yet supported')
     else:
         # #!# We should add a logger here.
-        raise Exception('Currently unsupported file type.')
+        raise NotImplementedError('Currently unsupported file type.')
 
     print('Reading the file')
     phys_in = populate_phys_input(infile, options.chtrig)
@@ -211,84 +212,84 @@ def _main(argv=None):
     # #!# Here the function viz.plot_channel should be called
     # for the desired channels.
 
-    # If file has to be processed, process it
-    if not options.info:
-
-        # #!# Get option of no trigger! (which is wrong practice or Respiract)
-        phys_in.check_trigger_amount(options.thr, options.num_tps_expected,
-                                     options.tr)
-        print('Checking that the output folder exists')
-        utils.path_exists_or_make_it(options.outdir)
-        print('Plot trigger')
-        viz.plot_trigger(phys_in.timeseries[0], phys_in.timeseries[1],
-                         outfile, options)
-
-        # The next few lines remove the undesired channels from phys_in.
-        if options.chsel:
-            print('Dropping unselected channels')
-            for i in reversed(range(0, phys_in.ch_amout)):
-                if i not in options.chsel:
-                    phys_in.delete_at_index(i)
-
-        # If requested, change channel names.
-        if options.ch_name:
-            print('Renaming channels with given names')
-            phys_in.rename_channels(options.ch_name)
-
-        # The next few lines create a dictionary of different blueprint_input
-        # objects, one for each unique frequency in phys_in
-        uniq_freq_list = set(phys_in.freq)
-        print(f'Found {len(uniq_freq_list)} unique frequencies.')
-        phys_out = {}
-        for uniq_freq in uniq_freq_list:
-            phys_out[uniq_freq] = deepcopy(phys_in)
-            for i in reversed(phys_in.freq):
-                if i != uniq_freq:
-                    phys_out[uniq_freq].delete_at_index(phys_in.ch_amount-i-1)
-
-        # Create a blueprint_output object for each unique frequency found.
+    # If only info were asked, end here.
+    if options.info:
+        return
+
+    # Run analysis on trigger channel to get first timepoint and the time offset.
+    # #!# Get option of no trigger! (which is wrong practice or Respiract)
+    phys_in.check_trigger_amount(options.thr, options.num_tps_expected,
+                                 options.tr)
+    print('Checking that the output folder exists')
+    utils.path_exists_or_make_it(options.outdir)
+    print('Plot trigger')
+    viz.plot_trigger(phys_in.timeseries[0], phys_in.timeseries[1],
+                     outfile, options)
+
+    # The next few lines remove the undesired channels from phys_in.
+    if options.chsel:
+        print('Dropping unselected channels')
+        for i in reversed(range(0, phys_in.ch_amout)):
+            if i not in options.chsel:
+                phys_in.delete_at_index(i)
+
+    # If requested, change channel names.
+    if options.ch_name is not None:
+        print('Renaming channels with given names')
+        phys_in.rename_channels(options.ch_name)
+
+    # The next few lines create a dictionary of different BlueprintInput
+    # objects, one for each unique frequency in phys_in
+    uniq_freq_list = set(phys_in.freq)
+    output_amount = len(uniq_freq_list)
+    if output_amount > 1:
+        print(f'Found {output_amount} different frequencies in input!')
+
+    print(f'Preparing {output_amount} output files.')
+    phys_out = {}
+    for uniq_freq in uniq_freq_list:
+        phys_out[uniq_freq] = deepcopy(phys_in)
+        for i in reversed(phys_in.freq):
+            if i != uniq_freq:
+                phys_out[uniq_freq].delete_at_index(phys_in.ch_amount-i-1)
+
+        # Also create a BlueprintOutput object for each unique frequency found.
         # Populate it with the corresponding blueprint input and replace it
         # in the dictionary.
-        for uniq_freq in uniq_freq_list:
-            phys_out[uniq_freq] = blueprint_output.init_from_blueprint(phys_out[uniq_freq])
+        phys_out[uniq_freq] = BlueprintOutput.init_from_blueprint(phys_out[uniq_freq])
 
-        output_amount = len(uniq_freq_list)
-        if output_amount > 1:
-            print(f'Found {output_amount} different frequencies in input!\n'
-                  f'Preparing {output_amount} output files')
+    if options.heur_file and options.sub:
+        print(f'Preparing BIDS output using {options.heur_file}')
+    elif options.heur_file and not options.sub:
+        print(f'While "-heur" was specified, option "-sub" was not.\n'
+              f'Skipping BIDS formatting.')
 
+    for uniq_freq in uniq_freq_list:
+        # If possible, prepare bids renaming.
         if options.heur_file and options.sub:
-            print(f'Preparing BIDS output using {options.heur_file}')
-        elif options.heur_file and not options.sub:
-            print(f'While "-heur" was specified, option "-sub" was not.\n'
-                  f'Skipping BIDS formatting.')
-
-        for uniq_freq in uniq_freq_list:
-            # If possible, prepare bids renaming.
-            if options.heur_file and options.sub:
-                if output_amount > 1:
-                    # Add "recording-freq" to filename if more than one freq
-                    outfile = use_heuristic(options.heur_file, options.sub,
-                                            options.ses, options.filename,
-                                            options.outdir, uniq_freq)
-                else:
-                    outfile = use_heuristic(options.heur_file, options.sub,
-                                            options.ses, options.filename,
-                                            options.outdir)
-
-            elif output_amount > 1:
-                # Append "freq" to filename if more than one freq
-                outfile = f'outfile_{uniq_freq}'
-
-            print('Exporting files for freq {uniq_freq}')
-            savetxt(outfile + '.tsv.gz', phys_out[uniq_freq].timeseries,
-                    fmt='%.8e', delimiter='\t')
-            print_json(outfile, phys_out[uniq_freq].freq,
-                       phys_out[uniq_freq].start_time,
-                       phys_out[uniq_freq].ch_name)
-            print_summary(options.filename, options.num_tps_expected,
-                          phys_in.num_tps_found, uniq_freq,
-                          phys_out[uniq_freq].start_time, outfile)
+            if output_amount > 1:
+                # Add "recording-freq" to filename if more than one freq
+                outfile = use_heuristic(options.heur_file, options.sub,
+                                        options.ses, options.filename,
+                                        options.outdir, uniq_freq)
+            else:
+                outfile = use_heuristic(options.heur_file, options.sub,
+                                        options.ses, options.filename,
+                                        options.outdir)
+
+        elif output_amount > 1:
+            # Append "freq" to filename if more than one freq
+            outfile = f'outfile_{uniq_freq}'
+
+        print('Exporting files for freq {uniq_freq}')
+        savetxt(outfile + '.tsv.gz', phys_out[uniq_freq].timeseries,
+                fmt='%.8e', delimiter='\t')
+        print_json(outfile, phys_out[uniq_freq].freq,
+                   phys_out[uniq_freq].start_time,
+                   phys_out[uniq_freq].ch_name)
+        print_summary(options.filename, options.num_tps_expected,
+                      phys_in.num_tps_found, uniq_freq,
+                      phys_out[uniq_freq].start_time, outfile)
 
 
 if __name__ == '__main__':
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 9b0b6df0a..66574296f 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -8,7 +8,7 @@
 import numpy as np
 
 
-def is_valid(var, var_type, list_type=None, return_var=True):
+def is_valid(var, var_type, list_type=None):
     """
     Checks that the var is of a certain type.
     If type is list and list_type is specified,
@@ -21,9 +21,6 @@ def is_valid(var, var_type, list_type=None, return_var=True):
         Type the variable is assumed to be.
     list_type: type
         Like var_type, but applies to list elements.
-    return_var: boolean
-        If true, the function returns the input variable.
-        Useful for checking over assignment.
 
     Output
     ------
@@ -35,10 +32,9 @@ def is_valid(var, var_type, list_type=None, return_var=True):
 
     if var_type is list and list_type is not None:
         for element in var:
-            is_valid(element, list_type, return_var=False)
+            _ = is_valid(element, list_type, return_var=False)
 
-    if return_var:
-        return var
+    return var
 
 
 def has_size(var, data_size, token):
@@ -47,7 +43,7 @@ def has_size(var, data_size, token):
     If it's not the case, fill in the var or removes exceding var entry.
     Input
     -----
-    var: any type
+    var: list
         Variable to be checked.
     data_size: int
         Size of data of interest.
@@ -58,20 +54,20 @@ def has_size(var, data_size, token):
 
     Output
     ------
-    var: any type
+    var: list
         Variable to be checked (same as input).
     """
     if len(var) > data_size:
         var = var[:data_size]
 
     if len(var) < data_size:
-        is_valid(token, type(var))
+        _ = is_valid(token, type(var[0]))
         var = var + [token] * (data_size - len(var))
 
     return var
 
 
-class blueprint_input():
+class BlueprintInput():
     """
     Main input object for phys2bids.
     Contains the blueprint to be populated.
@@ -145,14 +141,14 @@ def __init__(self, timeseries, freq, ch_name, units):
         self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')
 
-    def rename_channels(cls, new_names, ch_trigger=None):
+    def rename_channels(self, new_names, ch_trigger=None):
         """
         Renames the channels. If 'time' or 'trigger' were specified,
         it makes sure that they're the first and second entry.
 
         Input
         -----
-        cls: :obj: `blueprint_input`
+        self: :obj: `BlueprintInput`
             The object on which to operate
         new_names: list of str
             New names for channels.
@@ -161,7 +157,7 @@ def rename_channels(cls, new_names, ch_trigger=None):
 
         Outcome
         -------
-        cls.ch_name:
+        self.ch_name:
             Changes content to new_name.
         """
         if 'time' in new_names:
@@ -174,17 +170,17 @@ def rename_channels(cls, new_names, ch_trigger=None):
 
         new_names = ['time', 'trigger'] + new_names
 
-        cls.ch_name = has_size(is_valid(new_names, list, list_type=str),
-                               cls.ch_amount, 'unknown')
+        self.ch_name = has_size(is_valid(new_names, list, list_type=str),
+                                self.ch_amount, 'unknown')
 
-    def return_index(cls, idx):
+    def return_index(self, idx):
         """
         Returns the proper list entry of all the
         properties of the object, given an index.
 
         Input
         -----
-        cls: :obj: `blueprint_input`
+        self: :obj: `BlueprintInput`
             The object on which to operate
         idx: int
             Index of elements to return
@@ -195,40 +191,41 @@ def return_index(cls, idx):
             Tuple containing the proper list entry of all the
             properties of the object with index `idx`
         """
-        return (cls.timeseries[idx], cls.ch_amount, cls.freq[idx],
-                cls.ch_name[idx], cls.units[idx])
+        return (self.timeseries[idx], self.ch_amount, self.freq[idx],
+                self.ch_name[idx], self.units[idx])
 
-    def delete_at_index(cls, idx):
+    def delete_at_index(self, idx):
         """
         Returns all the proper list entry of the
         properties of the object, given an index.
 
         Input
         -----
-        cls: :obj: `blueprint_input`
+        self: :obj: `BlueprintInput`
             The object on which to operate
         idx: int or range
             Index of elements to delete from all lists
 
         Outcome
         -------
-        cls:
+        self:
             In all the property that are lists, the element correspondent to
             `idx` gets deleted
          """
-        del(cls.timeseries[idx])
-        del(cls.freq[idx])
-        del(cls.ch_name[idx])
-        del(cls.units[idx])
+        del(self.timeseries[idx])
+        del(self.freq[idx])
+        del(self.ch_name[idx])
+        del(self.units[idx])
+        self.ch_amount -= 1
 
-    def check_trigger_amount(cls, thr=2.5, num_timepoints_expected=0, tr=0):
+    def check_trigger_amount(self, thr=2.5, num_timepoints_expected=0, tr=0):
         """
         Counts trigger points and corrects time offset in
         the list representing time.
 
         Input
         -----
-        cls: :obj: `blueprint_input`
+        self: :obj: `BlueprintInput`
             The object on which to operate
         thr: float
             Threshold to be used to detect trigger points.
@@ -240,24 +237,24 @@ def check_trigger_amount(cls, thr=2.5, num_timepoints_expected=0, tr=0):
 
         Output
         ------
-        cls.num_timepoints_found: int
-            Property of the `blueprint_input` class.
+        self.num_timepoints_found: int
+            Property of the `BlueprintInput` class.
             Contains the number of timepoints found
             with the automatic estimation.
 
         Outcome
         -------
-        cls.timeseries:
+        self.timeseries:
             The property `timeseries` is shifted with the 0 being
             the time of first trigger.
         """
         print('Counting trigger points')
         # Use first derivative of the trigger channel to find the TRs,
         # comparing it to a given threshold.
-        trigger_deriv = np.diff(cls.timeseries[1])
+        trigger_deriv = np.diff(self.timeseries[1])
         timepoints = trigger_deriv > thr
         num_timepoints_found = timepoints.sum()
-        time_offset = cls.timeseries[0][timepoints.argmax()]
+        time_offset = self.timeseries[0][timepoints.argmax()]
 
         if num_timepoints_expected:
             print('Checking number of timepoints')
@@ -289,11 +286,11 @@ def check_trigger_amount(cls, thr=2.5, num_timepoints_expected=0, tr=0):
         else:
             print('Cannot check the number of timepoints')
 
-        cls.timeseries[0] -= time_offset
-        cls.num_timepoints_found = num_timepoints_found
+        self.timeseries[0] -= time_offset
+        self.num_timepoints_found = num_timepoints_found
 
 
-class blueprint_output():
+class BlueprintOutput():
     """
     Main output object for phys2bids.
     Contains the blueprint to be exported.
@@ -335,14 +332,14 @@ def __init__(self, timeseries, freq, ch_name, units, start_time):
         self.units = has_size(units, self.ch_amount, '[]')
         self.start_time = start_time
 
-    def return_index(cls, idx):
+    def return_index(self, idx):
         """
         Returns all the proper list entry of the
         properties of the object, given an index.
 
         Input
         -----
-        cls: :obj: `blueprint_output`
+        self: :obj: `BlueprintOutput`
             The object on which to operate
         idx: int
             Index of elements to return
@@ -353,47 +350,47 @@ def return_index(cls, idx):
             Tuple containing the proper list entry of all the
             properties of the object with index `idx`
         """
-        return (cls.timeseries[idx], cls.ch_amount, cls.freq,
-                cls.ch_name[idx], cls.units[idx], cls.start_time)
+        return (self.timeseries[idx], self.ch_amount, self.freq,
+                self.ch_name[idx], self.units[idx], self.start_time)
 
-    def delete_at_index(cls, idx):
+    def delete_at_index(self, idx):
         """
         Returns all the proper list entry of the
         properties of the object, given an index.
 
         Input
         -----
-        cls: :obj: `blueprint_output`
+        self: :obj: `BlueprintOutput`
             The object on which to operate
         idx: int or range
             Index of elements to delete from all lists
 
         Outcome
         -------
-        cls:
+        self:
             In all the property that are lists, the element correspondent to
             `idx` gets deleted
         """
-        del(cls.timeseries[idx])
-        del(cls.ch_name[idx])
-        del(cls.units[idx])
+        del(self.timeseries[idx])
+        del(self.ch_name[idx])
+        del(self.units[idx])
 
     @classmethod
     def init_from_blueprint(cls, blueprint):
         """
-        Method to populate the output blueprint using blueprint_input.
+        Method to populate the output blueprint using BlueprintInput.
 
         Input
         -----
-        cls: :obj: `blueprint_output`
+        cls: :obj: `BlueprintOutput`
             The object on which to operate
-        blueprint: :obj: `blueprint_input`
+        blueprint: :obj: `BlueprintInput`
             The input blueprint object
 
         Output
         ------
-        cls: :obj: `blueprint_output`
-            Populated `blueprint_output` object.
+        cls: :obj: `BlueprintOutput`
+            Populated `BlueprintOutput` object.
         """
         timeseries = np.asarray(blueprint.timeseries)
         freq = blueprint.freq[0]
diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 905887df9..62ce65d67 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -4,6 +4,8 @@
 import os
 import sys
 
+from pathlib import Path
+
 SUPPORTED_FTYPES = ('acq')  # , 'txt', 'mat', ...
 
 
@@ -21,10 +23,12 @@ def check_input_ext(filename, ext):
     """
     Checks that the given file has the given extension
     """
-    if filename[-len(ext):] != ext:
-        filename = filename + ext
-
-    return filename
+    if '.gz' in ext:
+        if filename[-len(ext):] != ext:
+            filename = filename + ext
+        return filename
+    else:
+        return Path(filename).with_suffix(ext)
 
 
 def check_input_type(filename, indir):
@@ -34,14 +38,14 @@ def check_input_type(filename, indir):
     """
     fftype_found = False
     for ftype in SUPPORTED_FTYPES:
-        filename = check_input_ext(filename, ftype)
-        if os.path.isfile(os.path.join(indir, filename)):
+        fname = check_input_ext(filename, ftype)
+        if os.path.isfile(os.path.join(indir, fname)):
             fftype_found = True
             break
 
     if fftype_found:
         print(f'File extension is .{ftype}')
-        return filename, ftype
+        return fname, ftype
     else:
         raise Exception(f'The file {filename} wasn\'t found in {indir}'
                         f' or {ftype} is not supported yet.\n'
@@ -67,7 +71,7 @@ def check_file_exists(filename):
 
 def print_info(filename, phys_object):
     """
-    Print the info of the input files, using blueprint_input object
+    Print the info of the input files, using BlueprintInput object
     """
     print(f'File {filename} contains:\n')
 

From e641231724f251dcb272a85cfc58a238fc3f8012 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Tue, 26 Nov 2019 23:39:03 +0100
Subject: [PATCH 31/42] Changed ch_name default from Nonetype to empty list

---
 phys2bids/cli/run.py   | 2 +-
 phys2bids/phys2bids.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/phys2bids/cli/run.py b/phys2bids/cli/run.py
index 4edf18e54..b2d3f7c1e 100644
--- a/phys2bids/cli/run.py
+++ b/phys2bids/cli/run.py
@@ -100,7 +100,7 @@ def _get_parser():
                           nargs='*',
                           type=str,
                           help='Columns header (for json file).',
-                          default=None)
+                          default=[])
 
     optional.add_argument('-v', '--version', action='version',
                           version=('%(prog)s ' + __version__))
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 5667a818e..13fc107ee 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -234,7 +234,7 @@ def _main(argv=None):
                 phys_in.delete_at_index(i)
 
     # If requested, change channel names.
-    if options.ch_name is not None:
+    if options.ch_name:
         print('Renaming channels with given names')
         phys_in.rename_channels(options.ch_name)
 

From d355bbdd3cc45cda5f840425fff212b98fc19809 Mon Sep 17 00:00:00 2001
From: Stefano Moia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 15:09:12 +0100
Subject: [PATCH 32/42] Assignment of empty `recording`

Co-Authored-By: Vicente Ferrer <38909338+vinferrer@users.noreply.github.com>
---
 phys2bids/phys2bids.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 13fc107ee..01aeca742 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -158,6 +158,7 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     heur = utils.load_heuristic(heur_file)
     name = heur.heur(filename[:-4], name)
 
+recording = ''
     if record_label:
         recording = f'_recording-{record_label}'
 

From b970ae3ee17246dbe0180b1a97e7adba6a30593e Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 16:57:55 +0100
Subject: [PATCH 33/42] Addressing @vinferrer 's review in PR #38, moving
 method from `utils.py` `physio_obj.py`.

---
 phys2bids/phys2bids.py  |  2 +-
 phys2bids/physio_obj.py | 23 +++++++++++++++++++++++
 phys2bids/utils.py      | 11 -----------
 3 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 01aeca742..4393dec1f 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -209,7 +209,7 @@ def _main(argv=None):
     print('Reading the file')
     phys_in = populate_phys_input(infile, options.chtrig)
     print('Reading infos')
-    utils.print_info(options.filename, phys_in)
+    phys_in.print_info(options.filename)
     # #!# Here the function viz.plot_channel should be called
     # for the desired channels.
 
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 66574296f..ecd72e60c 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -289,6 +289,29 @@ def check_trigger_amount(self, thr=2.5, num_timepoints_expected=0, tr=0):
         self.timeseries[0] -= time_offset
         self.num_timepoints_found = num_timepoints_found
 
+    def print_info(self, filename):
+        """
+        Print info on the file, channel by channel.
+
+        Input
+        -----
+        self: :obj: `BlueprintInput`
+            The object on which to operate
+        filename: str or path
+            Name of the input file to phys2bids
+
+        Outcome
+        -------
+        ch:
+            Returns to stdout (e.g. on screen) channels,
+            their names and their sampling rate.
+        """
+        print(f'File {filename} contains:\n')
+
+        for ch in range(2, self.ch_amount):
+            print(f'{(ch-2):02d}. {self.ch_name[ch]};'
+                  f' sampled at {self.freq[ch]} Hz')
+
 
 class BlueprintOutput():
     """
diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 62ce65d67..479332e11 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -69,17 +69,6 @@ def check_file_exists(filename):
         raise FileNotFoundError(f'The file {filename} does not exist!')
 
 
-def print_info(filename, phys_object):
-    """
-    Print the info of the input files, using BlueprintInput object
-    """
-    print(f'File {filename} contains:\n')
-
-    for ch in range(2, phys_object.ch_amount):
-        print(f'{(ch-2):02d}. {phys_object.ch_name[ch]};'
-              f' sampled at {phys_object.freq[ch]} Hz')
-
-
 def move_file(oldpath, newpath, ext=''):
     """
     Moves file from oldpath to newpath.

From a18b2b715f29c41c274cd5708a2935da2031075c Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 17:03:37 +0100
Subject: [PATCH 34/42] Keep addressing @vinferrer 's PR #38 review

---
 phys2bids/physio_obj.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index ecd72e60c..6aaa1750d 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -408,7 +408,8 @@ def init_from_blueprint(cls, blueprint):
         cls: :obj: `BlueprintOutput`
             The object on which to operate
         blueprint: :obj: `BlueprintInput`
-            The input blueprint object
+            The input blueprint object.
+            !!! All its frequencies should be the same !!!
 
         Output
         ------

From a257472d5b0da698c47af4fe31f30d56993b0238 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 18:28:16 +0100
Subject: [PATCH 35/42] Bug fix due to external commit

---
 phys2bids/phys2bids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 4393dec1f..734a522ed 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -158,7 +158,7 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     heur = utils.load_heuristic(heur_file)
     name = heur.heur(filename[:-4], name)
 
-recording = ''
+    recording = ''
     if record_label:
         recording = f'_recording-{record_label}'
 

From 056e0e15a87055d57343ea726350082cc850fa76 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 19:11:34 +0100
Subject: [PATCH 36/42] Bug fixes

---
 phys2bids/interfaces/acq.py | 1 +
 phys2bids/phys2bids.py      | 2 +-
 phys2bids/physio_obj.py     | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/phys2bids/interfaces/acq.py b/phys2bids/interfaces/acq.py
index 7ef73710e..d3554b6e3 100644
--- a/phys2bids/interfaces/acq.py
+++ b/phys2bids/interfaces/acq.py
@@ -27,5 +27,6 @@ def populate_phys_input(filename, chtrig):
             timeseries.append(ch.data)
             freq.append(ch.samples_per_second)
             units.append(ch.units)
+            names.append(ch.name)
 
     return BlueprintInput(timeseries, freq, names, units)
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 734a522ed..be7dbf39b 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -195,7 +195,7 @@ def _main(argv=None):
     infile = os.path.join(options.indir, options.filename)
     utils.check_file_exists(infile)
     outfile = os.path.join(options.outdir,
-                           os.path.basename(os.path.splitext(options.filename)))
+                           os.path.splitext(os.path.basename(options.filename))[0])
 
     # Read file!
     if ftype == 'acq':
diff --git a/phys2bids/physio_obj.py b/phys2bids/physio_obj.py
index 6aaa1750d..c9b285de9 100644
--- a/phys2bids/physio_obj.py
+++ b/phys2bids/physio_obj.py
@@ -32,7 +32,7 @@ def is_valid(var, var_type, list_type=None):
 
     if var_type is list and list_type is not None:
         for element in var:
-            _ = is_valid(element, list_type, return_var=False)
+            _ = is_valid(element, list_type,)
 
     return var
 

From d896d5b667b8baffd0db68d5092041e1d8ed04ff Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 19:12:22 +0100
Subject: [PATCH 37/42] Added check on extension entry in check_input_ext prior
 to Path().with_suffix()

---
 phys2bids/utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 479332e11..6dc1782cf 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -6,7 +6,7 @@
 
 from pathlib import Path
 
-SUPPORTED_FTYPES = ('acq')  # , 'txt', 'mat', ...
+SUPPORTED_FTYPES = ('acq', )  # 'txt', 'mat', ...
 
 
 def check_input_dir(indir):
@@ -28,6 +28,9 @@ def check_input_ext(filename, ext):
             filename = filename + ext
         return filename
     else:
+        if ext[0] != '.':
+            ext = '.' + ext
+
         return Path(filename).with_suffix(ext)
 
 

From 61b7f322dfbc69a94d65dc391d91aafae312ba00 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Wed, 27 Nov 2019 19:12:37 +0100
Subject: [PATCH 38/42] Added heuristic for acq test file

---
 phys2bids/heuristics/heur_test_acq.py | 54 +++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 phys2bids/heuristics/heur_test_acq.py

diff --git a/phys2bids/heuristics/heur_test_acq.py b/phys2bids/heuristics/heur_test_acq.py
new file mode 100644
index 000000000..a1e182b9b
--- /dev/null
+++ b/phys2bids/heuristics/heur_test_acq.py
@@ -0,0 +1,54 @@
+import sys
+import fnmatch
+
+
+def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
+    # ############################## #
+    # ##       Modify here!       ## #
+    # ##                          ## #
+    # ##  Possible variables are: ## #
+    # ##    -task (required)      ## #
+    # ##    -run                  ## #
+    # ##    -rec                  ## #
+    # ##    -acq                  ## #
+    # ##    -direct               ## #
+    # ##                          ## #
+    # ##                          ## #
+    # ##    See example below     ## #
+    # ############################## #
+
+    if fnmatch.fnmatchcase(physinfo, '*samefreq*.acq'):
+        task = 'test'
+        run = '00'
+        rec = 'biopac'
+    elif physinfo == 'Example':
+        task = 'rest'
+        run = '01'
+        acq = 'resp'
+        # ############################## #
+        # ## Don't modify below this! ## #
+        # ############################## #
+    else:
+        # #!# Transform sys.exit in debug warnings or raiseexceptions!
+        # #!# Make all of the above a dictionary
+        sys.exit()
+
+    if not task:
+        sys.exit()
+
+    name = name + '_task-' + task
+
+    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_recording-<label>]_physio
+    if acq:
+        name = name + '_acq-' + acq
+
+    if direct:
+        name = name + '_dir-' + direct
+
+    if rec:
+        name = name + '_rec-' + rec
+
+    if run:
+        name = name + '_run-' + run
+
+    return name

From 5ad1f3fb774215a38b9ee96e0f2c079015a87b65 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 28 Nov 2019 11:18:48 +0100
Subject: [PATCH 39/42] Bug fixing post-reviews

---
 phys2bids/cli/run.py   | 4 ++--
 phys2bids/phys2bids.py | 6 +++---
 phys2bids/viz.py       | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/phys2bids/cli/run.py b/phys2bids/cli/run.py
index b2d3f7c1e..475e327f5 100644
--- a/phys2bids/cli/run.py
+++ b/phys2bids/cli/run.py
@@ -81,7 +81,7 @@ def _get_parser():
                           help='The number corresponding to the channels to process.',
                           default=None)
     optional.add_argument('-ntp', '--numtps',
-                          dest='num_tps_expected',
+                          dest='num_timepoints_expected',
                           type=int,
                           help='Number of expected timepoints.',
                           default=0)
@@ -89,7 +89,7 @@ def _get_parser():
                           dest='tr',
                           type=float,
                           help='TR of sequence in seconds.',
-                          default=0)
+                          default=1)
     optional.add_argument('-thr', '--threshold',
                           dest='thr',
                           type=float,
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index be7dbf39b..01b456beb 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -219,7 +219,7 @@ def _main(argv=None):
 
     # Run analysis on trigger channel to get first timepoint and the time offset.
     # #!# Get option of no trigger! (which is wrong practice or Respiract)
-    phys_in.check_trigger_amount(options.thr, options.num_tps_expected,
+    phys_in.check_trigger_amount(options.thr, options.num_timepoints_expected,
                                  options.tr)
     print('Checking that the output folder exists')
     utils.path_exists_or_make_it(options.outdir)
@@ -288,8 +288,8 @@ def _main(argv=None):
         print_json(outfile, phys_out[uniq_freq].freq,
                    phys_out[uniq_freq].start_time,
                    phys_out[uniq_freq].ch_name)
-        print_summary(options.filename, options.num_tps_expected,
-                      phys_in.num_tps_found, uniq_freq,
+        print_summary(options.filename, options.num_timepoints_expected,
+                      phys_in.num_timepoints_found, uniq_freq,
                       phys_out[uniq_freq].start_time, outfile)
 
 
diff --git a/phys2bids/viz.py b/phys2bids/viz.py
index 3c022a089..e88204a78 100644
--- a/phys2bids/viz.py
+++ b/phys2bids/viz.py
@@ -34,8 +34,8 @@ def ntr2time(x):
     subplot.secondary_xaxis('top', functions=(time2ntr, ntr2time))
     subplot.plot(time, trigger, '-', time, time, '-')
     subplot = fig.add_subplot(224)
-    subplot.set_xlim([options.tr * (options.num_tps_expected - 4),
-                      options.tr * (options.num_tps_expected + 4)])
+    subplot.set_xlim([options.tr * (options.num_timepoints_expected - 4),
+                      options.tr * (options.num_timepoints_expected + 4)])
     subplot.set_ylim([-0.2, options.thr * 3])
     subplot.secondary_xaxis('top', functions=(time2ntr, ntr2time))
     subplot.plot(time, trigger, '-', time, time, '-')

From 3d1a47bab23f8e100060da60aa0361a96845c12f Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 28 Nov 2019 12:00:30 +0100
Subject: [PATCH 40/42] Corrected handling of path objects while using
 heuristics

---
 phys2bids/phys2bids.py | 8 ++++----
 phys2bids/utils.py     | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 01b456beb..4480cb8f7 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -28,12 +28,12 @@
 
 from copy import deepcopy
 from numpy import savetxt
+from pathlib import Path
 
 from phys2bids import utils, viz
 from phys2bids.cli.run import _get_parser
 from phys2bids.physio_obj import BlueprintOutput
 
-
 # #!# This is hardcoded until we find a better solution
 HEADERLENGTH = 9
 
@@ -114,13 +114,13 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
 
     Input
     -----
-    heur_file: str or path
+    heur_file: path
         Fullpath to heuristic file.
     sub: str or int
         Name of subject.
     ses: str or int or None
         Name of session.
-    filename: str
+    filename: path
         Name of the input of phys2bids.
     outdir: str or path
         Path to the directory that will become the "site" folder
@@ -156,7 +156,7 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     os.chdir(outdir)
 
     heur = utils.load_heuristic(heur_file)
-    name = heur.heur(filename[:-4], name)
+    name = heur.heur(Path(filename).stem, name)
 
     recording = ''
     if record_label:
diff --git a/phys2bids/utils.py b/phys2bids/utils.py
index 6dc1782cf..e4bf4ffb7 100644
--- a/phys2bids/utils.py
+++ b/phys2bids/utils.py
@@ -127,7 +127,7 @@ def load_heuristic(heuristic):
     Copied from [nipy/heudiconv](https://github.com/nipy/heudiconv)
     Copyright [2014-2019] [Heudiconv developers], Apache 2 license.
     """
-    if os.path.sep in heuristic or os.path.lexists(heuristic):
+    if os.path.lexists(heuristic):
         heuristic_file = os.path.realpath(heuristic)
         path, fname = os.path.split(heuristic_file)
         try:

From 5b7bd9d7aed65b061f0458527a950704c0725636 Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 28 Nov 2019 14:43:16 +0100
Subject: [PATCH 41/42] Changed use of heuristics

---
 phys2bids/heuristics/heur_test_acq.py | 4 ++--
 phys2bids/phys2bids.py                | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/phys2bids/heuristics/heur_test_acq.py b/phys2bids/heuristics/heur_test_acq.py
index a1e182b9b..3d3011732 100644
--- a/phys2bids/heuristics/heur_test_acq.py
+++ b/phys2bids/heuristics/heur_test_acq.py
@@ -17,7 +17,7 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
     # ##    See example below     ## #
     # ############################## #
 
-    if fnmatch.fnmatchcase(physinfo, '*samefreq*.acq'):
+    if fnmatch.fnmatchcase(physinfo, '*samefreq*'):
         task = 'test'
         run = '00'
         rec = 'biopac'
@@ -31,7 +31,7 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
     else:
         # #!# Transform sys.exit in debug warnings or raiseexceptions!
         # #!# Make all of the above a dictionary
-        sys.exit()
+        raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
 
     if not task:
         sys.exit()
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 4480cb8f7..beb516eb3 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -282,7 +282,7 @@ def _main(argv=None):
             # Append "freq" to filename if more than one freq
             outfile = f'outfile_{uniq_freq}'
 
-        print('Exporting files for freq {uniq_freq}')
+        print(f'Exporting files for freq {uniq_freq}')
         savetxt(outfile + '.tsv.gz', phys_out[uniq_freq].timeseries,
                 fmt='%.8e', delimiter='\t')
         print_json(outfile, phys_out[uniq_freq].freq,

From a80c6e90f8d7b0a6f942f98c6cb161c6b4a207df Mon Sep 17 00:00:00 2001
From: smoia <s.moia@bcbl.eu>
Date: Thu, 28 Nov 2019 14:49:58 +0100
Subject: [PATCH 42/42] Improved heuristic files

---
 phys2bids/heuristics/heur.py          | 10 +++-------
 phys2bids/heuristics/heur_ex.py       |  8 +++++---
 phys2bids/heuristics/heur_test_acq.py |  7 ++++---
 3 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/phys2bids/heuristics/heur.py b/phys2bids/heuristics/heur.py
index 443cb6efd..7b873dbab 100644
--- a/phys2bids/heuristics/heur.py
+++ b/phys2bids/heuristics/heur.py
@@ -48,18 +48,14 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
     else:
         # #!# Transform sys.exit in debug warnings or raiseexceptions!
         # #!# Make all of the above a dictionary
-        print('File not found in heuristics!\nExiting')
-        sys.exit()
+        raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
 
     if not task:
-        print('No "task" specified for this file!\nExiting')
-        sys.exit()
+        raise KeyError(f'No "task" attribute found')
 
     name = name + '_task-' + task
 
-    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>]
-    #                           [_ce-<label>][_dir-<label>][_rec-<label>]
-    #                           [_run-<index>][_recording-<label>]_physio
+    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_recording-<label>]_physio
     if acq:
         name = name + '_acq-' + acq
 
diff --git a/phys2bids/heuristics/heur_ex.py b/phys2bids/heuristics/heur_ex.py
index 2233f8a3a..52889629b 100644
--- a/phys2bids/heuristics/heur_ex.py
+++ b/phys2bids/heuristics/heur_ex.py
@@ -32,14 +32,16 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
     else:
         # #!# Transform sys.exit in debug warnings or raiseexceptions!
         # #!# Make all of the above a dictionary
-        sys.exit()
+        raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
 
     if not task:
-        sys.exit()
+        raise KeyError(f'No "task" attribute found')
 
     name = name + '_task-' + task
 
-    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_recording-<label>]_physio
+    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>] ...
+    #                ... [_ce-<label>][_dir-<label>][_rec-<label>] ...
+    #                ... [_run-<index>][_recording-<label>]_physio
     if acq:
         name = name + '_acq-' + acq
 
diff --git a/phys2bids/heuristics/heur_test_acq.py b/phys2bids/heuristics/heur_test_acq.py
index 3d3011732..eb8ba67d1 100644
--- a/phys2bids/heuristics/heur_test_acq.py
+++ b/phys2bids/heuristics/heur_test_acq.py
@@ -1,4 +1,3 @@
-import sys
 import fnmatch
 
 
@@ -34,11 +33,13 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
         raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
 
     if not task:
-        sys.exit()
+        raise KeyError(f'No "task" attribute found')
 
     name = name + '_task-' + task
 
-    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_recording-<label>]_physio
+    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>] ...
+    #                ... [_ce-<label>][_dir-<label>][_rec-<label>] ...
+    #                ... [_run-<index>][_recording-<label>]_physio
     if acq:
         name = name + '_acq-' + acq