diff --git a/matlab/dcm2niix4pet.m b/matlab/dcm2niix4pet.m index 6b2ac1e..fcd0a88 100644 --- a/matlab/dcm2niix4pet.m +++ b/matlab/dcm2niix4pet.m @@ -239,8 +239,6 @@ function dcm2niix4pet(FolderList,MetaList,varargin) end end - - %% convert % ---------- for folder = 1:size(FolderList,1) @@ -271,10 +269,8 @@ function dcm2niix4pet(FolderList,MetaList,varargin) telemetry_data.returncode = 1; telemetry(telemetry_data, folder); error('%s did not run properly',command) - end - - + % deal with dcm files dcmfiles = dir(fullfile(FolderList{folder},'*.dcm')); if isempty(dcmfiles) % since sometimes they have no ext :-( diff --git a/matlab/telemetry.m b/matlab/telemetry.m index 650837c..14532d5 100644 --- a/matlab/telemetry.m +++ b/matlab/telemetry.m @@ -52,7 +52,7 @@ function telemetry(telemetry_data, input_path, output_path) % if running in CI don't run telemetry running_in_ci = strcmpi(getenv("CI"), 'true'); - + if disable_telemetry | disable_telemetry_env | running_in_ci e = false; else diff --git a/matlab/updatejsonpetfile.m b/matlab/updatejsonpetfile.m index 3395d86..0aaaf8b 100644 --- a/matlab/updatejsonpetfile.m +++ b/matlab/updatejsonpetfile.m @@ -289,6 +289,11 @@ end filemetadata = update_arrays(filemetadata); + % set ModeOfAdministration to lower case + if isfield(filemetadata,'ModeOfAdministration') + filemetadata.ModeOfAdministration = lower(filemetadata.ModeOfAdministration); + end + % clean-up fn_check = fieldnames(filemetadata); for f=1:size(fn_check,1) diff --git a/pypet2bids/poetry.lock b/pypet2bids/poetry.lock index c3c274c..ae2937f 100644 --- a/pypet2bids/poetry.lock +++ b/pypet2bids/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. 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that # dcm2niix generates by default for PET imaging collect_these_fields = { diff --git a/pypet2bids/pypet2bids/ecat.py b/pypet2bids/pypet2bids/ecat.py index efbc2ea..a4f7988 100644 --- a/pypet2bids/pypet2bids/ecat.py +++ b/pypet2bids/pypet2bids/ecat.py @@ -453,6 +453,12 @@ def populate_sidecar(self, **kwargs): meta_radio_inputs = check_meta_radio_inputs(self.sidecar_template) self.sidecar_template.update(**meta_radio_inputs) + # set ModeOfAdministration to lower case + if self.sidecar_template.get("ModeOfAdministration", ""): + self.sidecar_template["ModeOfAdministration"] = self.sidecar_template[ + "ModeOfAdministration" + ].lower() + def prune_sidecar(self): """ Eliminate unpopulated fields in sidecar while leaving in mandatory fields even if they are unpopulated. diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py index 6ae54a9..b80d092 100644 --- a/pypet2bids/pypet2bids/telemetry.py +++ b/pypet2bids/pypet2bids/telemetry.py @@ -53,7 +53,10 @@ def telemetry_enabled(config_path=None): load_dotenv(dotenv_path=config_file) # check to see if telemetry is disabled - if os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false" or os.getenv("CI", "false") == "true": + if ( + os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false" + or os.getenv("CI", "false") == "true" + ): return False else: return True diff --git a/pypet2bids/pyproject.toml b/pypet2bids/pyproject.toml index 1ddf2cd..ab015b0 100644 --- a/pypet2bids/pyproject.toml +++ b/pypet2bids/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pypet2bids" -version = "1.3.14" +version = "1.3.15" description = "A python library for converting PET imaging and blood data to BIDS." authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"] license = "MIT"