Fixes to updatepetjson and ecatheaderupdate

pypet2bids/pypet2bids/ecat_header_update.py

@@ -4,10 +4,10 @@
     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
+    import pypet2bids.ecat as ecat
+    import pypet2bids.write_ecat as write_ecat
+    import pypet2bids.read_ecat as read_ecat
+    import pypet2bids.helper_functions as helper_functions
 
 # collect ecat header jsons
 ecat_headers = read_ecat.ecat_header_maps.get("ecat_headers")

pypet2bids/pypet2bids/update_json_pet_file.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from pathlib import Path
 from os.path import join
 from os import listdir
@@ -13,11 +15,15 @@
 
 try:
     import helper_functions
-    import is_pet
+    # The import of is_pet is deferred to get_metadata_from_spreadsheet() to 
+    # prevent circular import
+    #import is_pet
     import pet_metadata as metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
-    import pypet2bids.is_pet as is_pet
+    # The import of is_pet is deferred to get_metadata_from_spreadsheet() to 
+    # prevent circular import
+    #import pypet2bids.is_pet as is_pet
     import pypet2bids.pet_metadata as metadata
 
 # import logging
@@ -761,6 +767,12 @@ def get_metadata_from_spreadsheet(
     :return: dictionary of metadata
     :rtype: dict
     """
+    # Import is_pet here to avoid circular import
+    try:
+        import is_pet
+    except ModuleNotFoundError:
+        import pypet2bids.is_pet as is_pet
+
     spreadsheet_metadata = {"nifti_json": {}, "blood_json": {}, "blood_tsv": {}}
     spreadsheet_values = {}
     if Path(metadata_path).is_file():

pypet2bids/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pypet2bids"
-version = "1.4.4"
+version = "1.4.5"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = [
     {name = "anthony galassi", email = "[email protected]"}
@@ -64,8 +64,8 @@ convert-pmod-to-blood = "pypet2bids.convert_pmod_to_blood:main"
 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"
+updatepetjson = "pypet2bids.update_json_pet_file:update_json_cli"
+ecatheaderupdate = "pypet2bids.ecat_header_update:cli"
 
 [project.urls]
 Documentation = "https://pypet2bids.readthedocs.io/en/latest/"

spreadsheet_conversion/Readme.md

@@ -10,7 +10,7 @@ The example files, show the excel file and the resulting conversion as json.
 
 ## 1 spreadsheet for many subjects
 
-In most cases, you subjects are converted (say using dcm2niix) and you need to update the json files with the metadata for all subjects. This is easily acheived using our preformated [scanner excel sheet](https://github.com/openneuropet/PET2BIDS/blob/main/spreadsheet_conversion/many_subjects_sheet/scanner_metadata_template.xlsx) which applies that information to all and the [tracer related excel sheet](https://github.com/openneuropet/PET2BIDS/blob/main/spreadsheet_conversion/many_subjects_sheet/subjects_metadata_template.xlsx). 
+In most cases, you subjects are converted (say using dcm2niix) and you need to update the json files with the metadata for all subjects. This is easily achieved using our preformated [scanner excel sheet](https://github.com/openneuropet/PET2BIDS/blob/main/spreadsheet_conversion/many_subjects_sheet/scanner_metadata_template.xlsx) which applies that information to all and the [tracer related excel sheet](https://github.com/openneuropet/PET2BIDS/blob/main/spreadsheet_conversion/many_subjects_sheet/subjects_metadata_template.xlsx). 
 
 ## convert_spreadsheet_metadata.m