Merge pull request #365 from ISISNeutronMuon/fix-voronoi

Fix voronoi
ISISNeutronMuon · Mar 18, 2024 · 06716eb · 06716eb
2 parents 1f3f028 + 43f6153
commit 06716eb
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Showing 26 changed files with 652 additions and 150 deletions.
diff --git a/MDANSE/Src/MDANSE/Extensions/.gitignore b/MDANSE/Src/MDANSE/Extensions/.gitignore
@@ -1,14 +1,2 @@
-/distance_histogram.so
-/fast_calculation.so
-/mic_fast_calc.so
-/mt_fast_calc.so
-/qhull.so
-/sas_fast_calc.so
-/sd_fast_calc.so
-/distance_histogram.o
-/fast_calculation.o
-/mic_fast_calc.o
-/mt_fast_calc.o
-/qhull.o
-/sas_fast_calc.o
-/sd_fast_calc.o
+*.o
+*.so
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AxisSelectionConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AxisSelectionConfigurator.py
@@ -58,10 +58,16 @@ def configure(self, value):
             self.update(value)
 
         e1 = find_atoms_in_molecule(
-            trajConfig["instance"].universe, self["molecule"], self["endpoint1"], True
+            trajConfig["instance"]._chemical_system,
+            self["molecule"],
+            self["endpoint1"],
+            True,
         )
         e2 = find_atoms_in_molecule(
-            trajConfig["instance"].universe, self["molecule"], self["endpoint2"], True
+            trajConfig["instance"]._chemical_system,
+            self["molecule"],
+            self["endpoint2"],
+            True,
         )
 
         self["value"] = value

diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py
@@ -26,7 +26,7 @@ class HDFInputFileConfigurator(InputFileConfigurator):
     This configurator allows to input an HDF file as input file.
     """
 
-    _default = "INPUT_FILENAME.h5"
+    _default = "INPUT_FILENAME.mda"
 
     def __init__(self, name, variables=None, **kwargs):
         """
@@ -42,6 +42,7 @@ def __init__(self, name, variables=None, **kwargs):
         InputFileConfigurator.__init__(self, name, **kwargs)
 
         self._variables = variables if variables is not None else []
+        self._units = {}
 
     def configure(self, value):
         """
@@ -67,6 +68,10 @@ def configure(self, value):
         for v in self._variables:
             if v in self["instance"]:
                 self[v] = self["instance"][v][:]
+                try:
+                    self._units[v] = self["instance"][v].attrs["units"]
+                except:
+                    self._units[v] = "unitless"
             else:
                 self.error_status = (
                     f"the variable {v} was not  found in {value} HDF file"
@@ -87,7 +92,7 @@ def variables(self):
 
     def get_information(self):
         """
-        Returns some basic informations about the contents of theHDF file.
+        Returns some basic informations about the contents of the HDF file.
 
         :return: the informations about the contents of the HDF file.
         :rtype: str

diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py
@@ -16,6 +16,7 @@
 import os
 import tempfile
 import time
+from typing import Dict, Any
 
 from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import (
@@ -24,6 +25,26 @@
 )
 
 
+def parse_dictionary(input: str) -> Dict[str, Any]:
+    big_line = input.strip("\{\}[] \n")
+    tokens = big_line.split(",")
+    result = {}
+    for entry in tokens:
+        temp = entry.split(":")
+        key, value = temp[0], ":".join(temp[1:])
+        key = key.strip("' ")
+        value = value.strip(" '")
+        try:
+            value = int(value)
+        except:
+            try:
+                value = float(value)
+            except:
+                pass
+        result[key] = value
+    return result
+
+
 class McStasOptionsConfigurator(IConfigurator):
     """
     This configurator allows to input the McStas options that will be used to run a McStas executable file.
@@ -50,7 +71,9 @@ def configure(self, value):
 
         options = self._default.copy()
 
-        for k, v in list(value.items()):
+        parsed = parse_dictionary(value)
+
+        for k, v in list(parsed.items()):
             if k not in options:
                 continue
             options[k] = v

diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/McStasParametersConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/McStasParametersConfigurator.py
@@ -19,14 +19,15 @@
 
 from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
+from MDANSE.Framework.Configurators.McStasOptionsConfigurator import parse_dictionary
 
 
 class McStasParametersConfigurator(IConfigurator):
     """
     This configurator allows to input the McStas instrument parameters that will be used to run a McStas executable file.
     """
 
-    _mcStasTypes = {"double": float, "int": int, "StringConfigurator": str}
+    _mcStasTypes = {"double": float, "int": int, "string": str}
 
     _default = {
         "beam_wavelength_Angs": 2.0,
@@ -77,20 +78,27 @@ def configure(self, value):
             [exePath, "-h"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT
         )
 
+        parameters_bytes = s.communicate()[0]
+        parameters_string = parameters_bytes.decode(encoding="utf-8")
+
         instrParameters = dict(
             [
                 (v[0], [v[1], v[2]])
                 for v in re.findall(
-                    "\s*(\w+)\s*\((\w+)\)\s*\[default='(\S+)'\]", s.communicate()[0]
+                    "\s*(\w+)\s*\((\w+)\)\s*\[default='(\S+)'\]", parameters_string
                 )
                 if v[0] not in self._exclude
             ]
         )
 
         val = {}
-        for k, v in list(value.items()):
+        parsed = parse_dictionary(value)
+        print(f"Parsed input: {parsed}")
+        print(f"Received from McStas: {instrParameters}")
+        for k, v in list(parsed.items()):
             if k not in instrParameters:
-                instrParameters.pop(k)
+                # instrParameters.pop(k)  # how was that supposed to work?
+                continue
             val[k] = self._mcStasTypes[instrParameters[k][0]](v)
 
         self["value"] = ["%s=%s" % (k, v) for k, v in list(val.items())]

diff --git a/MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py b/MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py
@@ -1,5 +1,9 @@
 from MDANSE.Framework.Formats.IFormat import IFormat
-from MDANSE.Framework.OutputVariables import IOutputVariable
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from MDANSE.Framework.OutputVariables.IOutputVariable import IOutputVariable
 from .HDFFormat import HDFFormat
 
 
@@ -22,7 +26,7 @@ class MDAFormat(IFormat):
     def write(
         cls,
         filename: str,
-        data: dict[str, IOutputVariable],
+        data: dict[str, "IOutputVariable"],
         header: str = "",
         extension: str = extensions[0],
     ) -> None:

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/CoordinationNumber.py b/MDANSE/Src/MDANSE/Framework/Jobs/CoordinationNumber.py
@@ -29,6 +29,8 @@ class CoordinationNumber(DistanceHistogram):
 
     label = "Coordination Number"
 
+    enabled = True
+
     category = (
         "Analysis",
         "Structure",

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py
@@ -133,7 +133,7 @@ def run_step(self, index):
         variables = copy.deepcopy(current_configuration.variables)
         coords = variables.pop("coordinates")
         current_configuration = RealConfiguration(
-            trajectory.chemical_system, coords, None, **variables
+            trajectory.chemical_system, coords, **variables
         )
 
         trajectory.chemical_system.configuration = current_configuration