Merge pull request #293 from GSTT-CSC/release/1.0.5

Merge GSTT-CSC/release/1.0.5 into main

.github/workflows/test_cli.yml

@@ -42,12 +42,12 @@ jobs:
       - name: test acr_uniformity
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
         run: |
-          hazen task_acr_uniformity tests/data/acr/Siemens/Test --report
+          hazen acr_uniformity tests/data/acr/Siemens --report
       
       - name: test acr_ghosting
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
         run: |
-          hazen task_acr_ghosting tests/data/acr/Siemens/Test --report
+          hazen acr_ghosting 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

.gitignore

@@ -1,34 +1,46 @@
+# virtual environments
 hazen-venv
-.scannerwork
+/venv/
+
+# tests
 .coverage
 coverage.xml
+pytest-coverage.txt
+pytest.xml
+
+# cache
 **/__pycache__
 .idea
+.DS_Store
+/.cache/
+/.bash_history
+.pytest_cache
+
+# logs
 logs
 *.log
+Hazen_logger.log
+hazen.egg-info
+dist
+
+# data
 uploads
+*.png
+report
+# TODO: Remove the following if no longer needed
 tests/data/slicepos/results
 tests/data/uniformity/results
-rods.png
-tra_slicewidth5_Bottom_Profile.png
-tra_slicewidth5_Slice_Width_and_Distortion_Results.txt
-tra_slicewidth5_Slice_Width_and_Distortion_ROIs.png
-tra_slicewidth5_Top_Profile.png
-nodeids
-htmlcov
-build
-dist
-hazen.egg-info
+hazenlib/data
+
+# docs
 docs/_build
 docs/build
+build
+
+# mischellaneous
+# TODO: Remove the following if no longer needed
 hazen_getting_started.pdf
-.DS_Store
-/.cache/
-/.bash_history
 /junit.xml
-pytest-coverage.txt
-pytest.xml
-Hazen_logger.log
-*.png
-newdocs/_build
-/venv/
+.scannerwork
+nodeids
+htmlcov

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: "0.6.0"
+version: "1.0.5"
 ...

README.md

@@ -161,11 +161,10 @@ We have used hazen with MRI data from a handful of different MRI scanners, inclu
 
 The Release Manager should ensure:
 - All outstanding issues for the current release have been closed, or, transferred to future release.
-- All tests are passing on Github Actions.
+- All tests are passing on GitHub Actions.
 - All documentation has been updated with correct version numbers:
-   - Version number in `docs/conf.py`
-   - Version number in `hazenlib/__init__.py`
-   - Version number in `CITATION.cff`
+   - Update version number `hazenlib/_version.py`, i.e. imported into `docs/conf.py`, `hazenlib/__init__.py` and `setup.py`
+   - Update version number in `CITATION.cff`
 - The `release` branch has been merged into `main` branch
 - A new release has been created with a new version tag (tag = version number)
 

docs/source/conf.py

@@ -12,6 +12,8 @@
 #
 import os
 import sys
+from hazenlib import __version__
+
 sys.path.insert(0, os.path.abspath("../.."))
 
 
@@ -22,7 +24,7 @@
 author = 'Haris Shuaib'
 
 # The full version, including alpha/beta/rc tags
-release = '0.6.0'
+release = __version__
 
 
 # -- General configuration ---------------------------------------------------

hazenlib/HazenTask.py

@@ -10,11 +10,14 @@
 
 class HazenTask:
 
-    def __init__(self, data_paths: list, report: bool = False, report_dir: str = os.path.join(os.getcwd(), 'hazen_reports')):
+    def __init__(self, data_paths: list, report: bool = False, report_dir: str = os.path.join(os.getcwd(), 'report')):
         self.data_paths = sorted(data_paths)
         self.report: bool = report
         self.report_path = os.path.join(report_dir, type(self).__name__)
-        pathlib.Path(self.report_path).mkdir(parents=True, exist_ok=True)
+        if report:
+            pathlib.Path(self.report_path).mkdir(parents=True, exist_ok=True)
+        else:
+            pass
         self.report_files = []
 
     @property

hazenlib/__init__.py

@@ -74,12 +74,14 @@
 
 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>] [--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 -v|--version
+    hazen --version
 Options:
-    <task>    snr | slice_position | slice_width | spatial_resolution | uniformity | ghosting | relaxometry | snr_map
+    <task>    snr | slice_position | slice_width | spatial_resolution | uniformity | ghosting | relaxometry | snr_map |
+    acr_ghosting | acr_uniformity
     <folder>
     --report
 
@@ -360,6 +362,7 @@ def main():
 
     task = getattr(task_module, class_list[0].__name__)(data_paths=files,
                                                         report=arguments['--report'],
+                                                        # TODO: Is this necessary? See HazenTask __init__()
                                                         report_dir=[arguments['--output'] if arguments[
                                                             '--output'] else os.path.join(os.getcwd(), 'report')][0])
 
@@ -369,12 +372,14 @@ def main():
         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)
-    # Relaxometry not currently converted to HazenTask object - this task accessible in the CLI using the old syntax until it can be refactored
+    # 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)
-    # Relaxometry not currently converted to HazenTask object - this task accessible in the CLI using the old syntax until it can be refactored
+    # 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)]

hazenlib/_version.py

@@ -1 +1 @@
-__version__ = '1.0.4'
+__version__ = '1.0.5'

hazenlib/snr_map.py

@@ -28,6 +28,7 @@
 method for measurement of signal-to-noise ratio in MRI. Physics in Medicine
 & Biology, 58(11), 3775.
 """
+import pathlib
 
 import pydicom
 import numpy as np
@@ -361,7 +362,7 @@ def plot_summary(original_image, snr_map, roi_corners, roi_size):
 
 
 def main(dcm_list, kernel_len=9, roi_size=20, roi_distance=40,
-         report_path=False):
+         report_path=False, report_dir=pathlib.Path.joinpath(pathlib.Path.cwd(), 'report', 'SNRMap')):
     """
     Returns SNR parametric map on flood phantom DICOM file.
 
@@ -384,17 +385,21 @@ def main(dcm_list, kernel_len=9, roi_size=20, roi_distance=40,
     roi_distance : int, optional
         Distance from centre of image to centre of each ROI along both
         dimensions. The default is 40.
+    report_path:
+    report_dir:
 
     Returns
     -------
     results : dict
     """
-    # TODO
     # ----
     # * Scale ROI distance to account for different image sizes.
     # * Pass kernel_len and roi_size parameters from command line.
 
     results = {}
+    if report_path:
+        # Create nested report folder and ignore if already exists
+        pathlib.Path.mkdir(report_dir, parents=True, exist_ok=True)
 
     for dcm in dcm_list:
 
@@ -463,8 +468,8 @@ def main(dcm_list, kernel_len=9, roi_size=20, roi_distance=40,
         #  Save images
         #  ===========
         if report_path:
-            detailed_image_path = f'{report_path}_snr_map_detailed.png'
-            summary_image_path = f'{report_path}_snr_map.png'
+            detailed_image_path = pathlib.Path.joinpath(report_dir, f'{report_path}_snr_map_detailed.png')
+            summary_image_path = pathlib.Path.joinpath(report_dir, f'{report_path}_snr_map.png')
 
             fig_detailed.savefig(detailed_image_path, dpi=300)
             fig_summary.savefig(summary_image_path, dpi=300)

setup.py

@@ -1,7 +1,5 @@
 import setuptools
-import os
-
-__version__ = '1.0.4'
+from hazenlib import __version__
 
 install_requires = ['pydicom==2.2.2',
                     'numpy==1.21.4',

tests/__init__.py

@@ -2,3 +2,4 @@
 import pathlib
 
 TEST_DATA_DIR = pathlib.Path(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data'))
+TEST_REPORT_DIR = pathlib.Path(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'report'))

tests/test_acr_ghosting.py

@@ -3,8 +3,8 @@
 import pathlib
 import pydicom
 
-from hazenlib.tasks.task_acr_ghosting import ACRGhosting
-from tests import TEST_DATA_DIR
+from hazenlib.tasks.acr_ghosting import ACRGhosting
+from tests import TEST_DATA_DIR, TEST_REPORT_DIR
 
 
 class TestACRGhostingSiemens(unittest.TestCase):
@@ -13,8 +13,9 @@ class TestACRGhostingSiemens(unittest.TestCase):
     psg = 0.056
 
     def setUp(self):
-        self.acr_ghosting_task = ACRGhosting(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')])
-        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'Siemens', 'Test', '6.dcm'))
+        self.acr_ghosting_task = ACRGhosting(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')],
+                                             report_dir=pathlib.PurePath.joinpath(TEST_REPORT_DIR))
+        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'Siemens', '6.dcm'))
 
     def test_object_centre(self):
         assert self.acr_ghosting_task.centroid_com(self.dcm.pixel_array)[1] == self.centre
@@ -29,8 +30,9 @@ class TestACRGhostingGE(unittest.TestCase):
     psg = 0.487
 
     def setUp(self):
-        self.acr_ghosting_task = ACRGhosting(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')])
-        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'GE', 'Test', '4.dcm'))
+        self.acr_ghosting_task = ACRGhosting(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')],
+                                             report_dir=pathlib.PurePath.joinpath(TEST_REPORT_DIR))
+        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'GE', '4.dcm'))
 
     def test_object_centre(self):
         assert self.acr_ghosting_task.centroid_com(self.dcm.pixel_array)[1] == self.centre

tests/test_acr_uniformity.py

@@ -4,24 +4,25 @@
 import pydicom
 import numpy as np
 
-from hazenlib.tasks.task_acr_uniformity import ACRUniformity
-from tests import TEST_DATA_DIR
+from hazenlib.tasks.acr_uniformity import ACRUniformity
+from tests import TEST_DATA_DIR, TEST_REPORT_DIR
 
 
 class TestACRUniformitySiemens(unittest.TestCase):
     ACR_UNIFORMITY_DATA = pathlib.Path(TEST_DATA_DIR / 'acr')
     centre = [129, 128]
     piu = 68.66
-    array = np.zeros((256,256), dtype=int)
+    array = np.zeros((256, 256), dtype=int)
     array[127][126] = 1
     array[126][127] = 1
     array[127][127] = 1
     array[128][127] = 1
     array[127][128] = 1
 
     def setUp(self):
-        self.acr_uniformity_task = ACRUniformity(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')])
-        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'Siemens', 'Test', '6.dcm'))
+        self.acr_uniformity_task = ACRUniformity(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')],
+                                                 report_dir=pathlib.PurePath.joinpath(TEST_REPORT_DIR))
+        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'Siemens', '6.dcm'))
 
     def test_object_centre(self):
         assert self.acr_uniformity_task.centroid_com(self.dcm.pixel_array) == self.centre
@@ -32,7 +33,7 @@ def test_circular_mask(self):
 
     def test_uniformity(self):
         results = self.acr_uniformity_task.get_integral_uniformity(self.dcm)
-        assert round(results,2) == self.piu
+        assert round(results, 2) == self.piu
 
 
 # class TestACRUniformityPhilips(unittest.TestCase):
@@ -43,12 +44,13 @@ class TestACRUniformityGE(unittest.TestCase):
     piu = 84.76
 
     def setUp(self):
-        self.acr_uniformity_task = ACRUniformity(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')])
-        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'GE', 'Test', '4.dcm'))
+        self.acr_uniformity_task = ACRUniformity(data_paths=[os.path.join(TEST_DATA_DIR, 'acr')],
+                                                 report_dir=pathlib.PurePath.joinpath(TEST_REPORT_DIR))
+        self.dcm = pydicom.read_file(os.path.join(TEST_DATA_DIR, 'acr', 'GE', '4.dcm'))
 
     def test_object_centre(self):
         assert self.acr_uniformity_task.centroid_com(self.dcm.pixel_array) == self.centre
 
     def test_uniformity(self):
         results = self.acr_uniformity_task.get_integral_uniformity(self.dcm)
-        assert round(results,2) == self.piu
+        assert round(results, 2) == self.piu