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[FIX] update cli for preprocess #1190

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[FIX] update cli for preprocess #1190

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d72640e
update cli for preprocess
Remi-Gau Jan 25, 2024
f63c6c1
Merge remote-tracking branch 'upstream/main' into cli
Remi-Gau Jan 26, 2024
3500019
add stats command
Remi-Gau Jan 26, 2024
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19 changes: 19 additions & 0 deletions demos/openneuro/ds000001_run.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
#! /bin/bash

# script to run the demo via the command line
cd ../..

# bidspm demos/openneuro/inputs/ds000001 demos/openneuro/outputs/ds000001/derivatives subject \
# --action preprocess \
# --task balloonanalogrisktask \
# --fwhm 8 \
# --participant_label 01 02


bidspm demos/openneuro/inputs/ds000001 demos/openneuro/outputs/ds000001/derivatives subject \
--action stats \
--preproc_dir demos/openneuro/outputs/ds000001/derivatives/bidspm-preproc \
--task balloonanalogrisktask \
--model_file demos/openneuro/models/model-balloonanalogrisktaskDefault_smdl.json \
--fwhm 8 \
--participant_label 01 02
2 changes: 2 additions & 0 deletions src/bidspm.py
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Expand Up @@ -429,9 +429,11 @@ def run_command(cmd: str, platform: str | None = None) -> int:

if platform is None:
if Path(matlab()).exists():
log.info(f"Using matlab found at: {matlab()}")
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suggestion (llm): Logging the path to the Matlab executable is a good practice for debugging. However, calling matlab() function twice (once for logging and once for setting platform) could be inefficient if the function does any non-trivial computation or IO. Consider storing the result in a variable and reusing it.

platform = matlab()
cmd = cmd.replace(new_line, ", ")
else:
log.info("Using octave")
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suggestion (llm): Consistency in logging is important for maintainability. Consider adding the path to the octave executable, similar to how the path to Matlab is logged.

platform = "octave"

if platform == "octave":
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15 changes: 15 additions & 0 deletions src/cli/cliPreprocess.m
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Expand Up @@ -26,6 +26,21 @@ function cliPreprocess(varargin)
validate(args);

opt = getOptionsFromCliArgument(args);

if iscellstr(opt.taskName)
if numel(opt.taskName) > 1
logger('WARNING', ...
['Too many tasks for preprocessing.\n', ...
'bidspm can only preprocess one task at time.\n', ...
'To preprocess several tasks at once use fMRIprep.\n', ...
'Only taking the first one: ', opt.taskName{1}], ...
'options', opt, ...
'filename', mfilename, ...
'id', id);
end
opt.taskName = opt.taskName{1};
end

opt.pipeline.type = 'preproc';
opt = checkOptions(opt);

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4 changes: 2 additions & 2 deletions src/cli/inputParserForPreprocess.m
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Expand Up @@ -10,11 +10,11 @@
isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
isLogical = @(x) islogical(x) && numel(x) == 1;
isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x); %#ok<*ISCLSTR>
isEmptyOrisChar = @(x) isempty(x) || ischar(x); %#ok<*ISCLSTR>
isEmptyOrisCharOrCellstr = @(x) isempty(x) || ischar(x) || iscellstr(x); %#ok<*ISCLSTR>
isCellStr = @(x) iscellstr(x);

addParameter(args, 'space', {}, isCellStr);
addParameter(args, 'task', '', isEmptyOrisChar);
addParameter(args, 'task', '', isEmptyOrisCharOrCellstr);
addParameter(args, 'fwhm', 6, isPositiveScalar);
addParameter(args, 'dry_run', false, isLogical);
addParameter(args, 'anat_only', false, isLogical);
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2 changes: 1 addition & 1 deletion src/matlab.py
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Expand Up @@ -10,4 +10,4 @@ def matlab() -> str:

The 'matlab' executable is usually in the 'bin' subdirectory.
"""
return "/usr/local/MATLAB/R2018a/ bin/matlab"
return "/usr/local/MATLAB/R2018a/bin/matlab"
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