added small script to update ecat mainheader with, bump version (#270)

fixes issue #264

pypet2bids/pypet2bids/ecat_header_update.py

@@ -0,0 +1,68 @@
+try:
+    import ecat
+    import write_ecat
+    import read_ecat
+    import helper_functions
+except ImportError:
+    from pypet2bids.ecat import ecat
+    from pypet2bids.write_ecat import write_ecat
+    from pypet2bids.read_ecat import read_ecat
+    from pypet2bids import helper_functions
+
+# collect ecat header jsons
+ecat_headers = read_ecat.ecat_header_maps.get('ecat_headers')
+
+
+def update_ecat_header(ecat_file: str, new_values: dict):
+    """
+    Update the header of an ECAT file with new values
+    :param ecat_file: path to the ECAT file
+    :param new_values: dictionary of new values to update
+    :param ecat_header: dictionary of the ECAT header
+    :return: None
+    """
+
+    # read ecat and determine version of ecat file
+    print(f"Reading ECAT file {ecat_file}")
+    infile = ecat.Ecat(ecat_file)
+
+    # collect the appropriate header schema
+    sw_version = str(infile.ecat_header.get('SW_VERSION', 73))
+
+    infile_header_map = ecat_headers[sw_version]['mainheader']
+
+    # iterate through new values and update the header
+    for name, value in new_values.items():
+        if infile.ecat_header.get(name):
+            if type(infile.ecat_header[name]) == type(value):
+                infile.ecat_header[name] = value
+            else:
+                print(f"WARNING: {name} has type {type(infile.ecat_header[name])} "
+                      f"and new value {value} has type {type(value)}")
+        else:
+            print(
+                f"WARNING: {name} not found in header schema for ECAT {ecat_headers.ecat_header.get('SW_VERSION', 73)} "
+                f"not updating with value {value}")
+
+    # update the header of the ecat file in question
+    with open(infile.ecat_file, 'r+b') as outfile:
+        write_ecat.write_header(ecat_file=outfile,
+                                schema=infile_header_map,
+                                values=infile.ecat_header)
+
+
+def cli():
+    import argparse
+    parser = argparse.ArgumentParser(description='Update the header of an ECAT file')
+    parser.add_argument('ecat_file', type=str, help='path to the ECAT file')
+    parser.add_argument('new_values', nargs='*', action=helper_functions.ParseKwargs, default={},
+                        help='new values to update the MAINHEADER of the ecat file, e.g. NUM_FRAMES=71 '
+                             'or CALIBRATION_FACTOR=0.5. '
+                             'or STUDY_DESCRIPTION="very important work"'
+                             'If the value is a string, it must be in quotes.')
+    args = parser.parse_args()
+    update_ecat_header(ecat_file=args.ecat_file, new_values=args.new_values)
+
+
+if __name__ == '__main__':
+    cli()

pypet2bids/pypet2bids/write_ecat.py

@@ -59,7 +59,7 @@ def write_header(ecat_file, schema: dict, values: dict = {}, byte_position: int
         value_to_write = values.get(variable_name, None)
 
         # if no value is supplied in the value dict, pack with empty bytes as well
-        if not value_to_write:
+        if value_to_write is None:
             pack_empty = True
         # set variable to false if neither of these conditions is met
         else:

pypet2bids/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.2"
+version = "1.3.3"
 description = "A python implementation of an ECAT to BIDS converter."
 authors = ["anthony galassi <[email protected]>"]
 license = "MIT"
@@ -44,6 +44,7 @@ ispet = 'pypet2bids.is_pet:main'
 updatepetjsonfromdicom = 'pypet2bids.dcm2niix4pet:update_json_with_dicom_value_cli'
 updatepetjsonfromecat = 'pypet2bids.ecat_cli:update_json_with_ecat_value_cli'
 updatepetjson = 'pypet2bids.update_json:update_json_cli'
+ecatheaderupdate = 'pypet2bids.ecat_header_update:main'
 
 [tool.poetry.group.dev.dependencies]
 pyinstaller = "^5.4.1"