Merge pull request raamana#7 from sinhaharsh/master

Modify __str__ for BaseSequence

.github/workflows/continuous-integration.yml

@@ -31,11 +31,12 @@ jobs:
             -   name: Install dependencies
                 run: |
                     python -m pip install --upgrade pip
-                    if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
                     pip install .
+                    pip install .[test]
             -   name: Lint with flake8
                 run: |
                     make lint
             -   name: Test with pytest
+                working-directory: ${{ runner.temp }}
                 run: |
-                    pytest
+                    pytest --pyargs protocol

protocol/__init__.py

@@ -4,9 +4,10 @@
 
 __author__ = """Pradeep Reddy Raamana"""
 __email__ = '[email protected]'
-__version__ = '0.1.0'
+# __version__ = '0.1.0'
 
 import logging
+import sys
 
 from protocol.config import configure_logger
 
@@ -19,4 +20,18 @@
                              BASE_IMAGING_PARAMS_DICOM_TAGS,
                              ACRONYMS_IMAGING_PARAMETERS,
                              UnspecifiedType)
-from protocol.imaging import DicomImagingSequence, BidsImagingSequence, SiemensMRImagingProtocol, MRImagingProtocol
+from protocol.imaging import (DicomImagingSequence, BidsImagingSequence,
+                              SiemensMRImagingProtocol, MRImagingProtocol)
+
+try:
+    from protocol._version import __version__
+except ImportError:
+    if sys.version_info < (3, 8):
+        from importlib_metadata import version
+    else:
+        from importlib.metadata import version
+
+    try:
+        __version__ = version('protocol')
+    except Exception:
+        __version__ = "unknown"

protocol/base.py

@@ -801,7 +801,8 @@ def __str__(self):
         for key in self.params:
             param = self.__dict__[key]
             name = param.acronym if param.acronym else param.name
-            plist.append(f'{name}={param._value}')
+            if not isinstance(param.get_value(), UnspecifiedType):
+                plist.append(f'{name}={param.get_value()}')
 
         return '{}({})'.format(self.name, ','.join(plist))
 

protocol/config.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 
 
-def configure_logger(log, output_dir, mode='w', level='WARNING'):
+def configure_logger(log, output_dir, mode='w', level='ERROR'):
     """
     Initiate log files.
 
@@ -29,7 +29,7 @@ def configure_logger(log, output_dir, mode='w', level='WARNING'):
     error_formatter = '%(asctime)s - %(levelname)s - %(message)s'
     if output_dir is None:
         output_dir = tempfile.gettempdir()
-    output_dir = Path(output_dir) / '.mrdataset'
+    output_dir = Path(output_dir) / '.protocol'
     output_dir.mkdir(parents=True, exist_ok=True)
 
     options = {
@@ -161,6 +161,7 @@ def __repr__(self):
     'PartialFourier'                : (0x18, 0x9081),
     'PartialFourierDirection'       : (0x18, 0x9036),
     'PhaseEncodingDirection'        : (0x18, 0x1312),
+    'InPlanePhaseEncodingDirection' : (0x18, 0x1312),
 
     # Timing Parameters
     'EchoTime'                      : (0x18, 0x81),
@@ -172,7 +173,7 @@ def __repr__(self):
     'FlipAngle'                     : (0x18, 0x1314),
 
     # Slice Acceleration Parameters
-    'MultiBandAccelerationFactor'   : (0x43, 0x1083),
+    'MultibandAccelerationFactor'   : (0x43, 0x1083),
 
     # Misc Parameters
     'BodyPartExamined'              : (0x18, 0x15),
@@ -254,7 +255,7 @@ def __repr__(self):
     'DwellTime'                     : 'DT',
     'RepetitionTime'                : 'TR',
     'FlipAngle'                     : 'FA',
-    'MultiBandAccelerationFactor'   : 'MAF',
+    'MultibandAccelerationFactor'   : 'MAF',
     'BodyPartExamined'              : 'BPE',
     'EchoTrainLength'               : 'ETL',
     'PixelBandwidth'                : 'PBW',
@@ -303,6 +304,8 @@ def __repr__(self):
     'PositivePCSDirections'         : 'PPCSD',
     'FieldOfView'                   : 'FOV',
     'ImageType'                     : 'IT',
+    'InPlanePhaseEncodingDirection' : 'PPED',
+    'EffectiveEchoSpacing'          : 'EES',
 }
 
 ACRONYMS_DEMOGRAPHICS = {
@@ -317,6 +320,34 @@ def __repr__(self):
     "ContentTime"    : "CT",
 }
 
+PARAMETERS_ANALOGUES = {
+    'InPlanePhaseEncodingDirection': [
+        'InPlanePhaseEncodingDirectionDICOM',
+    ],
+    'ManufacturersModelName': [
+        'ManufacturerModelName',
+    ],
+    'PhaseEncodingSteps'    : [
+        'NumberOfPhaseEncodingSteps',
+    ],
+    'PercentPhaseFOV'       : [
+        'PercentPhaseFieldOfView',
+    ],
+
+}
+
+INVALID_PARAMETERS = [
+    'DatasetType', 'License', 'Authors', 'Acknowledgements',
+    'HowToAcknowledge', 'Funding', 'ReferencesAndLinks',
+    'DatasetDOI', 'EthicsApprovals', 'ClinicalTrials',
+    'Name', 'Description', 'BIDSVersion',
+]
+
+# Invert the dictionary to get the reverse mapping
+PARAMETERS_ANALOGUES_DICT = {val: key
+                             for key, values in PARAMETERS_ANALOGUES.items()
+                             for val in values}
+
 BASE_IMAGING_PARAMETER_NAMES = list(BASE_IMAGING_PARAMS_DICOM_TAGS.keys())
 
 # Constant dicom Identifiers used to extract dicom headers