Minor bugfixes

Author: marcelzwiers

bidscoin/bids.py

@@ -710,7 +710,7 @@ def __repr__(self):
     def __eq__(self, other):
         """A shallow test if the DataType name is equal (so irrespective whether their runitems differ)"""
 
-        if isinstance(other, Union[DataType, str]):
+        if isinstance(other, DataType) or isinstance(other, str):
             return str(self) == str(other)
         else:
             return NotImplemented
@@ -867,10 +867,14 @@ def remove_datatype(self, datatype: Union[str, DataType]):
             self._data.pop(datatype, None)
             LOGGER.bcdebug(f"The '{datatype}' datatype was removed from {self}")
 
-    def delete_runs(self, datatype: Union[str, DataType]):
-        """Delete all run-items from the datatype section"""
+    def delete_runs(self, datatype: Union[str, DataType]=''):
+        """Delete all run-items from the dataformat or only from a datatype section"""
 
-        self._data[str(datatype)] = []
+        if not datatype:
+            for datatype in self.datatypes:
+                self.delete_runs(datatype)
+        else:
+            self._data[str(datatype)] = []
 
 
 class BidsMap:
@@ -1461,8 +1465,7 @@ def delete_runs(self):
         """Delete all run-items from the bidsmap"""
 
         for dataformat in self.dataformats:
-            for datatype in dataformat.datatypes:
-                dataformat.delete_runs(datatype)
+            dataformat.delete_runs()
 
     def insert_run(self, runitem: RunItem, position: int=None):
         """
@@ -1751,7 +1754,7 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
 
     Another hack is to get 'PhaseEncodingDirection` (see https://neurostars.org/t/determining-bids-phaseencodingdirection-from-dicom/612/10)
 
-    :param tagname:     DICOM attribute name (e.g. 'SeriesNumber') or Pydicom-style tag number (e.g. '0x00200011', '(0x20,0x11)', '(0020, 0011)')
+    :param tagname:     DICOM attribute name (e.g. 'SeriesNumber') or Pydicom-style tag number (e.g. '0x00200011', '(0x20,0x11)', '(0020,0011)')
     :param dicomfile:   The full pathname of the dicom-file
     :return:            Extracted tag-values as a flat string
     """
@@ -1810,7 +1813,7 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
                     # XA enhanced DICOM hack: Catch missing EchoNumbers from the private ICE_Dims field (0x21, 0x1106)
                     if tagname in ('EchoNumber', 'EchoNumbers') and not value:
                         for elem in dicomdata.iterall():
-                            if elem.tag == (0x21, 0x1106):
+                            if elem.tag == (0x21,0x1106):
                                 value = elem.value.split('_')[1] if '_' in elem.value else ''
                                 LOGGER.bcdebug(f"Parsed `EchoNumber(s)` from Siemens ICE_Dims `{elem.value}` as: {value}")
                                 break

bidscoin/utilities/physio.py

@@ -209,7 +209,7 @@ def readphysio(fn: Union[str,Path]) -> dict:
         LOGGER.verbose(f"Reading physio DICOM file: {fn}")
         dicomdata    = dcmread(fn, force=True)          # The DICM tag may be missing for anonymized DICOM files
         manufacturer = dicomdata.get('Manufacturer')
-        physiotag    = tag.Tag(0x7fe1, 0x1010)          # A private Siemens tag
+        physiotag    = tag.Tag(0x7FE1,0x1010)          # A private Siemens tag
         if manufacturer and 'SIEMENS' not in manufacturer.upper():
             LOGGER.warning(f"Unsupported manufacturer: '{manufacturer}', this function is designed for SIEMENS advanced physiological logging data")
         if (dicomdata.get('ImageType')==['ORIGINAL','PRIMARY','RAWDATA','PHYSIO'] and dicomdata.get(physiotag).private_creator=='SIEMENS CSA NON-IMAGE') or \

docs/bidsmap.rst

@@ -111,7 +111,7 @@ The run-items in the default 'bidsmap_dccn' template bidsmap have values that ar
    - Make a copy of the DCCN template (``[home]/.bidscoin/[version]/templates/bidsmap_dccn.yaml``) as a starting point for your own template bidsmap, and adapt it to your needs. You can set your copy as the new default template by editing the ``[home]/.bidscoin/config.toml`` file. Default templates and config file are automatically recreated from source when deleted
    - The power of regular expressions is nearly unlimited, you can e.g. use `negative look aheads <https://docs.python.org/3/howto/regex.html#lookahead-assertions>`__ to **not** match (exclude) certain strings
    - When creating new run-items, make sure to adhere to the YAML format and to the definitions in the BIDS schema files (``[path_to_bidscoin]/bidscoin/schema/datatypes``). You can test your YAML syntax using an online `YAML-validator <https://www.yamllint.com>`__ and your compliance with the BIDS standard with ``bidscoin -t your_template_bidsmap``. If all seems well you can install it using ``bidscoin -i your_template_bidsmap``.
-   - In addition to DICOM attribute names, the more advanced/unambiguous pydicom-style `tag numbers <https://pydicom.github.io/pydicom/stable/old/base_element.html#tag>`__ can also be used for indexing a DICOM header. For instance, the ``PatientName``, ``0x00100010``, ``0x10,0x10``, ``(0x10, 0x10)``, and ``(0010, 0010)`` index keys are all equivalent.
+   - In addition to DICOM attribute names, the more advanced/unambiguous pydicom-style `tag numbers <https://pydicom.github.io/pydicom/stable/old/base_element.html#tag>`__ can also be used for indexing a DICOM header. For instance, the ``PatientName``, ``0x00100010``, ``0x10,0x10``, ``(0x10,0x10)``, and ``(0010,0010)`` index keys are all equivalent.
 
 Editing the template bidsmap
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

tests/test_bids.py

@@ -93,10 +93,10 @@ def test_dynamicvalue(self, datasource):
         assert datasource.dynamicvalue(r'<<PatientName:.*\^(.*?)1>>')                            == r'<<PatientName:.*\^(.*?)1>>'
         assert datasource.dynamicvalue(r'<<PatientName:.*\^(.*?)1>>', runtime=True)              == 'MR'
         assert datasource.dynamicvalue(r'pat-<PatientName:.*\^(.*?)1>I<filename:MR_(.*?)\.dcm>') == 'patMRIsmall'
-        assert datasource.dynamicvalue(r"<Patient's Name>")                                      == 'CompressedSamplesMR1'    # Patient's Name, 0x00100010, 0x10,0x10, (0x10, 0x10), and (0010, 0010) index keys are all equivalent
+        assert datasource.dynamicvalue(r"<Patient's Name>")                                      == 'CompressedSamplesMR1'    # Patient's Name, 0x00100010, 0x10,0x10, (0x10,0x10), and (0010,0010) index keys are all equivalent
         assert datasource.dynamicvalue(r'<0x00100010>')                                          == 'CompressedSamplesMR1'
         assert datasource.dynamicvalue(r'<0x10,0x10>')                                           == 'CompressedSamplesMR1'
-        assert datasource.dynamicvalue(r'<(0x10, 0x10)>')                                        == 'CompressedSamplesMR1'
+        assert datasource.dynamicvalue(r'<(0x10,0x10)>')                                         == 'CompressedSamplesMR1'
         assert datasource.dynamicvalue(r'<(0010,0010)>')                                         == 'CompressedSamplesMR1'