Merge branch 'release/1.1.2'

.github/ISSUE_TEMPLATE/bug_report.md

@@ -24,9 +24,10 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
+ - OS: [e.g. macOS 12.1]
+ - Python version [e.g. 3.6, 3.8]
+ - Hazen version [e.g. 0.6.0]
+ - Deployment [e.g. Docker, venv, web]
 
 **Additional context**
 Add any other context about the problem here.

.github/workflows/publish_docker.yml

@@ -23,12 +23,12 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@57396166ad8aefe6098280995947635806a0e6ea
+        uses: docker/metadata-action@507c2f2dc502c992ad446e3d7a5dfbe311567a96
         with:
           images: gsttmriphysics/hazen
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@c56af957549030174b10d6867f20e78cfd7debc5
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
         with:
           context: .
           push: true

.github/workflows/test_cli.yml

@@ -39,6 +39,12 @@ jobs:
           hazen snr tests/data/snr/Siemens --report
           hazen snr tests/data/snr/Siemens --measured_slice_width 5.0012 --report
 
+      - name: test_acr_snr
+        if: always() # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_snr tests/data/acr/Siemens --report
+          hazen acr_snr tests/data/acr/Siemens --subtract tests/data/acr/Siemens2 --report
+
       - name: test acr_uniformity
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
         run: |
@@ -48,6 +54,16 @@ jobs:
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
         run: |
           hazen acr_ghosting tests/data/acr/Siemens --report
+          
+      - name: test acr_slice_position
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_slice_position tests/data/acr/Siemens --report
+
+      - name: test acr_geometric_accuracy
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen acr_geometric_accuracy tests/data/acr/Siemens --report
 
       - name: test slice_position
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
@@ -80,3 +96,9 @@ jobs:
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
         run: |
           hazen snr_map tests/data/snr/Siemens --report
+
+      - name: test relaxometry
+        if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
+        run: |
+          hazen relaxometry tests/data/relaxometry/T1/site1_20200218/plate5 --calc_t1 --plate_number=5 --report
+

CITATION.cff

@@ -43,5 +43,5 @@ date-released: 2022-02-24
 message: "If you use hazen in your work, please cite it using these metadata."
 repository-code: "https://github.com/GSTT-CSC/hazen"
 title: hazen
-version: "1.1.0"
+version: "1.1.2"
 ...

MANIFEST.in

@@ -0,0 +1,2 @@
+graft hazenlib/data
+graft hazenlib/tasks/data

README.md

@@ -7,7 +7,7 @@
 <p align="center">
 Quality assurance framework for Magnetic Resonance Imaging
 <br />
-<a href="https://github.com/github_username/repo_name"><strong>Explore the docs »</strong></a>
+<a href="https://hazen.readthedocs.io/en/latest/"><strong>Explore the docs »</strong></a>
 <br />
 <br />
 <a href="https://github.com/GSTT-CSC/hazen">View repo</a>
@@ -40,7 +40,7 @@ Some example outputs from hazen:
 
 | hazen snr                        | hazen ghosting                |
 |----------------------------------|-------------------------------|
-| ![](docs/assets/snr-example.png) | ![](docs/assets/ghosting.png) |
+| ![](docs/assets/SNR.png) | ![](docs/assets/ghosting.png) |
 
 ---
 

contributors.txt

@@ -1,4 +1,5 @@
 Paul Wilson
+Yassine Azma
 Laurence Jackson
 Dika Vilic
 Elizabeth Gabriel
@@ -7,5 +8,4 @@ Neil Heraghty
 Siân Culley
 Tom Roberts
 Lucrezia Cester
-Siân Culley
 Haris Shuaib

hazenlib/__init__.py

@@ -74,18 +74,21 @@
 
 Welcome to the Hazen Command Line Interface
 Usage:
-    hazen <task> <folder> [--measured_slice_width=<mm>] [--report] [--output=<path>] [--calc_t1 | --calc_t2]
-    [--plate_number=<n>] [--show_template_fit]
+    hazen <task> <folder> [--measured_slice_width=<mm>] [--subtract=<folder2>] [--report] [--output=<path>]
+    [--calc_t1 | --calc_t2] [--plate_number=<n>] [--show_template_fit]
     [--show_relax_fits] [--show_rois] [--log=<lvl>] [--verbose]
     hazen -h|--help
     hazen --version
 Options:
+Report is an optional argument needed if you want to get a plot of your results.
+'Calc_t1', 'calc_t', 'plate_number=<n>', 'show_template_fit', 'show_relax_fits', 'show_rois', 'verbose' are optional arguments for the relaxometry function.
+'Measured_slice_width' is an optional argument for the SNR function.
+'Log' is an optional argument that allows users to set the severity of the logs.
     <task>    snr | slice_position | slice_width | spatial_resolution | uniformity | ghosting | relaxometry | snr_map |
-    acr_ghosting | acr_uniformity
+    acr_ghosting | acr_uniformity |
     <folder>
     --report
 
-
 """
 import importlib
 import inspect
@@ -333,7 +336,6 @@ def parse_relaxometry_data(task, arguments, dicom_objects,
 def main():
     arguments = docopt(__doc__, version=__version__)
     task_module = importlib.import_module(f"hazenlib.tasks.{arguments['<task>']}")
-
     files = get_dicom_files(arguments['<folder>'])
     pp = pprint.PrettyPrinter(indent=4, depth=1, width=1)
 
@@ -368,22 +370,26 @@ def main():
 
     if not arguments['<task>'] == 'snr' and arguments['--measured_slice_width']:
         raise Exception("the (--measured_slice_width) option can only be used with snr")
+    elif not arguments['<task>'] == 'acr_snr' and arguments['--subtract']:
+        raise Exception("the (--subtract) option can only be used with acr_snr")
     elif arguments['<task>'] == 'snr' and arguments['--measured_slice_width']:
         measured_slice_width = float(arguments['--measured_slice_width'])
         logger.info(f'Calculating SNR with measured slice width {measured_slice_width}')
         result = task.run(measured_slice_width)
+    elif arguments['<task>'] == 'acr_snr':
+        acr_snr_cli_args = {'--subtract'}
+
+        acr_snr_args = {}
+        for key in acr_snr_cli_args:
+            acr_snr_args[key[2:]] = arguments[key]
+
+        result = task.run(**acr_snr_args)
     # TODO: Refactor Relaxometry task into HazenTask object Relaxometry not currently converted to HazenTask object -
     #  this task accessible in the CLI using the old syntax until it can be refactored
     elif arguments['<task>'] == 'relaxometry':
         task = importlib.import_module(f"hazenlib.{arguments['<task>']}")
         dicom_objects = [pydicom.read_file(x, force=True) for x in files if is_dicom_file(x)]
         result = parse_relaxometry_data(task, arguments, dicom_objects, report=True)
-    # TODO: Refactor SNR Map into HazenTask object (if not already) Relaxometry not currently converted to HazenTask
-    #  object - this task accessible in the CLI using the old syntax until it can be refactored
-    elif arguments['<task>'] == 'snr_map':
-        task = importlib.import_module(f"hazenlib.{arguments['<task>']}")
-        dicom_objects = [pydicom.read_file(x, force=True) for x in files if is_dicom_file(x)]
-        result = task.main(dicom_objects, report_path=True)
     else:
         result = task.run()
 

hazenlib/_version.py

@@ -1 +1 @@
-__version__ = '1.1.0'
+__version__ = '1.1.2'