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added script to create jsons files for MP2RAGE #101

Merged
merged 15 commits into from
Nov 2, 2018
Merged

added script to create jsons files for MP2RAGE #101

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bbd5a92
added script to create jsons files for MP2RAGE
Remi-Gau Oct 3, 2018
8fb02cf
remove unecessary block quotes
Remi-Gau Oct 18, 2018
eacb65e
made OrderedDict declaration more human readable
Remi-Gau Oct 18, 2018
63a6da1
made comments more transparent
Remi-Gau Oct 18, 2018
248976a
made file naming relative to end index of the mag image of the first …
Remi-Gau Oct 18, 2018
6cf0137
remove hard coded values
Remi-Gau Oct 19, 2018
7481d73
remove dead code
Remi-Gau Oct 19, 2018
1e21cfd
implement string slit to get basename of files to create
Remi-Gau Oct 19, 2018
258cd26
implement glob instead of walk to get subject folder list
Remi-Gau Oct 19, 2018
b46c5f0
Linting, update line lengths
emdupre Oct 26, 2018
c2f7d5c
Use py3 glob features
emdupre Oct 26, 2018
f45dc86
bring start_dir declaration at top of the script
Remi-Gau Oct 29, 2018
3258e35
[ENH] Switch to functions for writing json files
emdupre Oct 31, 2018
d56d6b1
Merge branch 'MP2RAGE-jsons' into enh/create-functions
emdupre Nov 1, 2018
bbd0e0d
Merge pull request #2 from emdupre/enh/create-functions
Remi-Gau Nov 2, 2018
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136 changes: 136 additions & 0 deletions pythonCode/create_MP2RAGE_json.py
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"""
WARNING:
This script was created in October 2018 when the specification
for MP2RAGE files was not fully finalized. Please double check with
latest version of the specs to make sure this is accurate.

This script will create the JSON files required for an MP2RAGE file.
To function it requires a BIDS data set with properly named image files:
The script will through all the folders of a BIDS data set and will create
the JSON files in every folder where it finds a file ending
with '_MPRAGE.nii.gz'.

Created by RG 2018-10-03
"""

import os
import json
from shutil import copyfile
from collections import OrderedDict

'''
DEFINE CONTENT OF JSON FILES
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Since these are single line comments, can you just do them in the # format rather than as block quotes ?

'''
# sub-*_inv-1_MPRAGE.json
data_inv_1 = OrderedDict()
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One option that might be a little cleaner -- since you know all of the key-value pairs at the start, you could include all of them in the definition. So here, for data_inv_1, you might do:

data_inv_1 = OrderedDict([
      ('InversionTime', '900'),
      ('FlipAngle', '5')
])

Totally stylistic, but might be nice from a human readability perspective !

data_inv_1['InversionTime'] = '900' # ms
data_inv_1['FlipAngle'] = '5'

# sub-*_inv-2_MPRAGE.json
data_inv_2 = OrderedDict()
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Same thing for this dictionary !

data_inv_2['InversionTime'] = '2750' # ms
data_inv_2['FlipAngle'] = '3'

# sub-*_T1map.json
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Could you remove these lines since they're unused and not clarifying comments ?

# sub-*_T1w.json
data_T1 = OrderedDict()
data_T1['EstimationMethod'] = 'Marques et al., 2013'


# sub-*_MPRAGE.json
data_MP2RAGE = OrderedDict()
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Same stylistic comment is above -- you can really see the difference here with many fields !

data_MP2RAGE['MagneticFieldStrength'] = ''
data_MP2RAGE['ExcitationRepetitionTime'] = ''
data_MP2RAGE['InversionRepetitionTime'] = ''
data_MP2RAGE['NumberShots'] = ''
data_MP2RAGE['Manufacturer'] = ''
data_MP2RAGE['ManufacturersModelName'] = ''
data_MP2RAGE['DeviceSerialNumber'] = ''
data_MP2RAGE['SoftwareVersions'] = ''
data_MP2RAGE['StationName'] = ''
data_MP2RAGE['InstitutionName'] = ''
data_MP2RAGE['InstitutionAddress'] = ''
data_MP2RAGE['InstitutionalDepartmentName'] = ''
data_MP2RAGE['ReceiveCoilName'] = ''
data_MP2RAGE['ReceiveCoilActiveElements'] = ''
data_MP2RAGE['GradientSetType'] = ''
data_MP2RAGE['MRTransmitCoilSequence'] = ''
data_MP2RAGE['MatrixCoilMode'] = ''
data_MP2RAGE['CoilCombinationMethod'] = ''
data_MP2RAGE['NonlinearGradientCorrection'] = ''
data_MP2RAGE['WaterFatShift'] = ''
data_MP2RAGE['EchoTrainLength'] = ''
data_MP2RAGE['DwellTime'] = ''
data_MP2RAGE['MultibandAccelerationFactor'] = ''
data_MP2RAGE['AnatomicalLandmarkCoordinates'] = ''
data_MP2RAGE['MRAcquisitionType'] = ''
data_MP2RAGE['ScanningSequence'] = ''
data_MP2RAGE['SequenceVariant'] = ''
data_MP2RAGE['ScanOptions'] = ''
data_MP2RAGE['SequenceName'] = ''
data_MP2RAGE['PulseSequenceType'] = 'MP2RAGE'
data_MP2RAGE['PulseSequenceDetails'] = ''
data_MP2RAGE['ParallelReductionFactorInPlane'] = ''
data_MP2RAGE['ParallelAcquisitionTechnique'] = ''
data_MP2RAGE['PartialFourier'] = ''
data_MP2RAGE['PartialFourierDirection'] = ''
data_MP2RAGE['EffectiveEchoSpacing'] = ''
data_MP2RAGE['TotalReadoutTime'] = ''
data_MP2RAGE['PhaseEncodingDirection'] = ''
data_MP2RAGE['EchoTime1'] = '' # sec
data_MP2RAGE['EchoTime2'] = '' # sec
data_MP2RAGE['SliceThickness'] = '' # mm


'''
WRITE THEM
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Same thing here about single-line comments !

'''
start_dir = "" # insert here path to your BIDS data set

# list all subjects
subj_ls = next(os.walk(start_dir))[1]
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instead of using os.walk, have you thought about using glob ? It's another standard import and might be a little cleaner, here !

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Still gotta do that one.


for iSubj in subj_ls:
print(iSubj)
# list all subfolders and files for that subject
subj_dir = os.walk(os.path.join(start_dir, iSubj))
# go through all the files for that subject
for path, subdirs, files in subj_dir:
for name in files:
# creates the json files in the folder where the the MP2RAGE file is found
if '_MPRAGE.nii.gz' in name:
print(os.path.join(path, name))

json_folder = path

# _inv-1_MPRAGE.json
json_name = name[:12] + '_inv-1_MPRAGE.json'
# create the file
with open(os.path.join(json_folder, json_name), 'w') as ff:
json.dump(data_inv_1, ff, sort_keys=False, indent=4)

# _inv-2_MPRAGE.json
json_name = name[:12] + '_inv-2_MPRAGE.json'
with open(os.path.join(json_folder, json_name), 'w') as ff:
json.dump(data_inv_2, ff, sort_keys=False, indent=4)

# _MPRAGE.json
json_name = name[:12] + '_MPRAGE.json'
with open(os.path.join(json_folder, json_name), 'w') as ff:
json.dump(data_MP2RAGE, ff, sort_keys=False, indent=4)

# sub-01_T1map.json
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I'm not sure if these are clarifying or not ! Could you add more text, if they're intended to be ?

# sub-01_T1w.json
data_T1['BasedOn'] = \
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This is a little hard to read -- could you define these strings first and then assign them as a value to this key ?

os.path.join('anat', name[:12] + '_inv1_part-mag_MPRAGE.nii.gz') + ', ' + \
os.path.join('anat', name[:12] + '_inv1_part-phase_MPRAGE.nii.gz') + ', ' + \
os.path.join('anat', name[:12] + '_inv1_part-mag_MPRAGE.nii.gz') + ', ' + \
os.path.join('anat', name[:12] + '_inv1_part-phase_MPRAGE.nii.gz') + ', '

json_name = name[:12] + '_T1map.json'
with open(os.path.join(json_folder, json_name), 'w') as ff:
json.dump(data_T1, ff, sort_keys=False, indent=4)

json_name = name[:12] + '_T1w.json'
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I can't test this locally right now, so just to confirm -- why is it name[:12] ?

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why is it name[:12]
Well spotted! That was one issue I had to fix. The script will now write the JSON files if it finds a _inv1_part-mag_MPRAGE.nii.gz and the name of the JSON files to create can then be based on the end index of that file without worrying how people decide to name their subjects / session...

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@emdupre emdupre Oct 18, 2018 •
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Ah, I see now ! One other way to do this, then, that might be a little clearer -- something like:

sid = '_'.join(name.split('_')[:-3])  # excludes last three key-value pairs

Avoiding counting characters just eases the cognitive burden when reading the code ! And writing it, too :)

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Also, then, rather calling e.g. name[:-29] multiple times, you could just assign the above string to a value and pop that in as you need it ✨

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Thanks for the feedback: helps me learn new stuff! Will implement that and directory walking today hopefully.
Also the multiple calling is definitely a bad habit from years of matlab coding: gotta lose that one fast!

with open(os.path.join(json_folder, json_name), 'w') as ff:
json.dump(data_T1, ff, sort_keys=False, indent=4)