merge_fig_css.py

"""
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merge_fig_css.py
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Goal of the script:
Concat all pycortex maps and prf figures of one subject in one pdf
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Input(s):
sys.argv[1]: main project directory
sys.argv[2]: project name (correspond to directory)
sys.argv[3]: number of subjects
sys.argv[4]: group
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Output(s):
one pdf file with pycortex maps and one pdf file with prf figures
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To run:
0. To Run on meso (not on node)
1. cd to function
>>  cd ~/projects/[PROJECT]/analysis_code/postproc/prf/postfit
2. run python command
>> python merge_fig_css.py [main directory] [project name] [subject num] [group]
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Exemple:
cd ~/projects/pRF_analysis/analysis_code/postproc/prf/postfit

python merge_fig_css.py /scratch/mszinte/data MotConf sub-01 327
python merge_fig_css.py /scratch/mszinte/data MotConf sub-170k 327
python merge_fig_css.py /scratch/mszinte/data MotConf group 327

python merge_fig_css.py /scratch/mszinte/data RetinoMaps sub-01 327
python merge_fig_css.py /scratch/mszinte/data RetinoMaps sub-170k 327
python merge_fig_css.py /scratch/mszinte/data RetinoMaps group 327

python merge_fig_css.py /scratch/mszinte/data amblyo_prf sub-01 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf sub-170k 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group_patient 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group_aniso 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group_mixed 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group_strab 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group_control 327
python merge_fig_css.py /scratch/mszinte/data amblyo_prf group_excluded 327
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Written by Uriel Lascombes (uriel.lascombes@laposte.net)
Edited by Martin Szinte (mail@martinszinte.net)
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"""
# General imports
import os
import sys
import json
import glob
from pypdf import PdfWriter

# Debug
import ipdb
deb = ipdb.set_trace

# Inputs
main_dir = sys.argv[1]
project_dir = sys.argv[2]
subject = sys.argv[3]
group = sys.argv[4]

# load settings
base_dir = os.path.abspath(os.path.join(os.getcwd(), "../../../../"))
settings_path = os.path.join(base_dir, project_dir, "settings.json")

with open(settings_path) as f:
    json_s = f.read()
    analysis_info = json.loads(json_s)
if subject == 'sub-170k': 
    formats = ['170k']
    extensions = ['dtseries.nii']
else: 
    formats = analysis_info['formats']
    extensions = analysis_info['extensions']
prf_task_name = analysis_info['prf_task_name']

# Merge Pycortex Maps
for format_, extension in zip(formats, extensions):   
    # Defind output directory and file
    prf_merge_dir = '{}/{}/derivatives/pp_data/{}/{}/figures/prf'.format(
        main_dir, project_dir, subject, format_)
    os.makedirs(prf_merge_dir, exist_ok = True)
    pycortex_merge_fn = '{}_prf-all_maps.pdf'.format(subject)
    
    # Find all pycortex maps 
    pycortex_roi_dir = '{}/{}/derivatives/pp_data/{}/{}/rois/pycortex/flatmaps_rois/*'.format(
        main_dir, project_dir, subject, format_)
    pycortex_corr_dir = '{}/{}/derivatives/pp_data/{}/{}/corr/pycortex/flatmaps_inter-run-corr/*{}*'.format(
        main_dir, project_dir, subject, format_, prf_task_name)
    pycortex_gauss_dir = '{}/{}/derivatives/pp_data/{}/{}/prf/pycortex/flatmaps_avg_gauss_gridfit/*'.format(
        main_dir, project_dir, subject, format_)
    pycortex_css_dir = '{}/{}/derivatives/pp_data/{}/{}/prf/pycortex/flatmaps_css_loo-median/*'.format(
        main_dir, project_dir, subject, format_)
    
    pycortex_all = glob.glob(pycortex_roi_dir) \
        + glob.glob(pycortex_corr_dir) \
            + glob.glob(pycortex_gauss_dir) \
                + glob.glob(pycortex_css_dir)
    
    # Merge pdf and export final pdf 
    if 'group' not in subject:
        pycortex_merger = PdfWriter()
        for n_page, pycortex_map in enumerate(pycortex_all): 
            # merge
            pycortex_merger.append(pycortex_map)
            
        # Export the pdf 
        merge_fn = "{}/{}".format(prf_merge_dir, pycortex_merge_fn)
        print("Saving {}".format(merge_fn))
        pycortex_merger.write(merge_fn)
        pycortex_merger.close()

    # Merge prf figures
    # Defind output directory and file
    prf_fig_merge_fn = '{}_prf-all_fig.pdf'.format(subject)

    # Find all prf figures  
    prf_fig_dir = '{}/{}/derivatives/pp_data/{}/{}/prf/figures/*'.format(
        main_dir, project_dir, subject, format_)
    prf_fig_dir_fns = glob.glob(prf_fig_dir)

    # Merge pdf and export final pdf 
    figures_merger = PdfWriter()
    for n_page, figure_fn in enumerate(prf_fig_dir_fns): 
        # merge
        figures_merger.append(figure_fn)
        
    # Export the pdf   
    merge_fn = '{}/{}'.format(prf_merge_dir, prf_fig_merge_fn)
    print("Saving {}".format(merge_fn))
    figures_merger.write(merge_fn)
    figures_merger.close()
    
# Define permission cmd
print('Changing files permissions in {}/{}'.format(main_dir, project_dir))
os.system("chmod -Rf 771 {}/{}".format(main_dir, project_dir))
os.system("chgrp -Rf {} {}/{}".format(group, main_dir, project_dir))