diff --git a/LICENSE.txt b/LICENSE.txt index 60debb11..10863683 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,21 +1,678 @@ -MIT License - -Copyright (c) 2017 Christophe Bedetti - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index c426dd54..4adf8c72 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ Dcm2Bids helps you to convert DICOM files of a study to [Brain Imaging Data Stru Learn more about BIDS and read the [specifications][bids-spec]. -# Install +## Install ``` git clone https://github.com/cbedetti/Dcm2Bids @@ -12,57 +12,32 @@ git clone https://github.com/cbedetti/Dcm2Bids Add the installation directory to your PYTHONPATH and the `scripts` directory to your PATH. -### Software dependencies +#### Software dependencies -- [dcm2niix][dcm2niix-github] with `dcm2niibatch` compiled +- dcm2niix -### Python dependencies +DICOM to NIfTI conversion is done with `dcm2niix` converter. See their [github][dcm2niix-github] for source or [NITRC][dcm2niix-nitrc] for compiled versions. -The file `environment.yml` contains the python dependencies. It's possible to create a `dcm2bids` python environment with [conda][conda]. +## Usage ``` -conda config --add channels conda-forge -conda env create -f environment.yml +dcm2bids [-h] -d DICOM_DIR -p PARTICIPANT [-s SESSION] -c CONFIG + [--dry_dcm2niix] [-y] ``` -# Usage - -``` -dcm2bids [-h] -o BIDS_DIR -d DICOM_DIR -p PARTICIPANT [-s SESSION] -c CONFIG [-n] -``` - -You need to build the config file of your study to let `dcm2bids` associate your acquisitions with the right dicoms through dicom header fields. Every study is different and this step needs a little bit of work. +You need to build the config file of your study to let `dcm2bids` associate your acquisitions with the right dicoms through bids sidecar created by dcm2niix. Every study is different and this step needs a little bit of work. The configuration uses the `json` format and one example is provided in the `example` directory. -### batch options - -``` -{ - "batch_options": { - "isGz": true, - "isFlipY": false, - "isVerbose": false, - "isCreateBIDS": true, - "isOnlySingleFile": false - } -} -``` - -This is the options needed for `dcm2niibatch`. Keep them like that. - -### descriptions +#### Descriptions The description field is a list of dictionnary. Each dictionnary describes one acquisition. -# Output - -The script creates a batch file and save it in the `code` directory of your BIDS folder. It execute automatically `dcm2niibatch` after that. It is possible to do a dry run if you add the option `-n`. - -# DICOM to NIfTI conversion +#### Output -Conversion is done with `dcm2niibatch`, a tool from dcm2niix converter. See their [github][dcm2niix-github] for source or [NITRC][dcm2niix-nitrc] for compiled versions. +dcm2bids create `sub-` directories in the folder the script is launched. +Acquisitions with no or more than one fitting descriptions are kept in `tmp_dcm2niix` directory. Users can review these missing acquistions to change the configuration file accordingly. [bids]: http://bids.neuroimaging.io/ [bids-spec]: http://bids.neuroimaging.io/#download diff --git a/dcm2bids/batch.py b/dcm2bids/batch.py deleted file mode 100644 index 1af9df84..00000000 --- a/dcm2bids/batch.py +++ /dev/null @@ -1,62 +0,0 @@ -# -*- coding: utf-8 -*- - - -from subprocess import call -import os -import yaml - - -def make_directory_tree(directory): - if not os.path.exists(directory): - os.makedirs(directory) - - -class Batch(object): - """ - """ - - def __init__(self, options, bidsDir, participant): - self.options = options - self.bidsDir = bidsDir - self.participant = participant - self.files = [] - self.codeDir = os.path.join(os.path.abspath(bidsDir), 'code') - self.yaml = os.path.join( - self.codeDir, "{}.yml".format(participant.prefix)) - - - def add(self, acquisition): - filename = "{}_{}".format(self.participant.prefix, acquisition.suffix) - in_dir = os.path.relpath( - os.path.dirname(acquisition.dicomPath), - self.codeDir) - out_dir = os.path.relpath(os.path.join( - self.bidsDir, - self.participant.directory, - acquisition.dataType), self.codeDir) - self.files.append({ - "filename": filename, - "in_dir": in_dir, - "out_dir": out_dir, - }) - - - def write(self): - make_directory_tree(self.codeDir) - data = {"Options": self.options, "Files": self.files} - with open(self.yaml, 'w') as f: - yaml.dump(data, f, default_flow_style=False, indent=4) - - - def show(self): - with open(self.yaml, 'r') as f: - print(f.read()) - - - def execute(self): - command = "dcm2niibatch {}".format(self.yaml) - os.chdir(self.codeDir) - for f in self.files: - make_directory_tree(f["out_dir"]) - call(command, shell=True) - diff --git a/dcm2bids/dcm2bids.py b/dcm2bids/dcm2bids.py index c12c173b..a885c96c 100644 --- a/dcm2bids/dcm2bids.py +++ b/dcm2bids/dcm2bids.py @@ -1,31 +1,24 @@ # -*- coding: utf-8 -*- +import glob import os -import json -from .batch import Batch -from .dcmparser import Dcmparser -from .structure import Acquisition, Participant - - -def load_json(filename): - with open(filename, 'r') as f: - data = json.load(f) - return data +from builtins import input +from .dcm2niix import Dcm2niix +from .sidecarparser import Sidecarparser +from .structure import Participant +from .utils import load_json, make_directory_tree, splitext_ class Dcm2bids(object): """ """ - def __init__(self, bids_dir, dicom_dir, config, participant, - session=None, dryrun=False): + def __init__(self, dicom_dir, config, yes, participant, session=None): self.dicomDir = dicom_dir self.config = load_json(config) + self.yes = yes self.participant = Participant(participant, session) - self.batch = Batch( - self.config["batch_options"], bids_dir, self.participant) - self.dryrun = dryrun @property @@ -36,46 +29,48 @@ def session(self): def session(self, value): self.participant.session = value - @property - def options(self): - if "dcm2bids_options" in self.config: - return self.config["dcm2bids_options"] - else: - return {} - @property - def force(self): - if "force" in self.options: - return self.options["force"] - else: - return False - - - def acquisitions(self): - for root, dirs, files in os.walk(self.dicomDir): - for f in sorted(files): - if f.startswith('.') == True: - continue - else: - dicomPath = os.path.join(root, f) - dcm = Dcmparser(dicomPath, self.force) - if dcm.isDicom(): - yield dcm.search_from(self.config["descriptions"]) - break - else: - continue + def run(self): + dcm2niix = Dcm2niix(self.dicomDir, self.participant) + dcm2niix.run() + parser = Sidecarparser(dcm2niix.sidecars, self.config["descriptions"]) + for acq in parser.acquisitions: + state = self._move(acq) + if state != 0: return state + return 0 + + + def _move(self, acquisition): + targetDir = os.path.join( + os.getcwd(), self.participant.directory, acquisition.dataType) + filename = "{}_{}".format(self.participant.prefix, acquisition.suffix) + targetBase = os.path.join(targetDir, filename) + + targetNiigz = targetBase + ".nii.gz" + if os.path.isfile(targetNiigz) and not self.yes: + reply = self._ask(targetNiigz) + if reply == "q": + return 1 + elif reply == "a": + self.yes = True + + make_directory_tree(targetDir) + for f in glob.glob(acquisition.base + ".*"): + _, ext = splitext_(f) + os.rename(f, targetBase + ext) - def run(self): - for acquisition in self.acquisitions(): - if acquisition is not None: - self.batch.add(acquisition) - else: - pass - self.batch.write() - if self.dryrun: - self.batch.show() - else: - self.batch.execute() return 0 + + def _ask(self, target): + print("") + print("'{}' already exists".format(os.path.basename(target))) + print("This file will be erase and replace if you continue") + while True: + p = "Do you want to (q)uit, (c)ontinue or continue for (a)ll? " + reply = input(p) + if reply == "c" or reply == "q" or reply == "a": + break + return reply + diff --git a/dcm2bids/dcm2niix.py b/dcm2bids/dcm2niix.py new file mode 100644 index 00000000..5797cb62 --- /dev/null +++ b/dcm2bids/dcm2niix.py @@ -0,0 +1,43 @@ +# -*- coding: utf-8 -*- + + +import glob +import os +from subprocess import call +from .utils import clean + + +class Dcm2niix(object): + """ + """ + + def __init__(self, dicom_dir, participant=None): + self.dicomDir = dicom_dir + self.participant = participant + self.options = "-b y -ba y -z y -f '%f_%p_%t_%s'" + self.sidecars = [] + + + @property + def outputDir(self): + if self.participant is None: + return os.path.join(os.getcwd(), 'tmp_dcm2bids', "config_help") + else: + return os.path.join( + os.getcwd(), 'tmp_dcm2bids', self.participant.prefix) + + + def run(self): + clean(self.outputDir) + self.execute() + self.sidecars = glob.glob(os.path.join(self.outputDir, "*.json")) + self.sidecars.sort() + return 0 + + + def execute(self): + commandStr = "dcm2niix {} -o {} {}" + command = commandStr.format( + self.options, self.outputDir, self.dicomDir) + call(command, shell=True) + diff --git a/dcm2bids/dcmparser.py b/dcm2bids/dcmparser.py deleted file mode 100644 index 47f193fd..00000000 --- a/dcm2bids/dcmparser.py +++ /dev/null @@ -1,88 +0,0 @@ -# -*- coding: utf-8 -*- - - -from future.utils import iteritems -import dicom -from dicom.errors import InvalidDicomError -from .structure import Acquisition - - -class Dcmparser(object): - - def __init__(self, dicomPath, force=False): - self.ds = None - self.dicomPath = dicomPath - self.force = force - - - def isDicom(self): - try: - self.ds = dicom.read_file(self.dicomPath, force=self.force) - except InvalidDicomError: - self.ds = None - return self.ds is not None - - - def search_from(self, descriptions): - for description in descriptions: - if self._respect(description["criteria"]): - acq = Acquisition( - self.dicomPath, - description["dataType"], - description["suffix"]) - if "customLabels" in description: - acq.customLabels = description["customLabels"] - else: - acq.customLabels = None - return acq - #No criteria respecting the dicom informations - return None - - - def _respect(self, criteria): - isEqual = "equal" in criteria - isIn = "in" in criteria - - # Check if there is some criteria - if not any([isEqual, isIn]): - return False - - if isEqual: - rsl_equal = self._isEqual(criteria["equal"]) - else: - rsl_equal = True - - if isIn: - rsl_in = self._isIn(criteria["in"]) - else: - rsl_in = True - - return all([rsl_equal, rsl_in]) - - - def _isEqual(self, criteria): - rsl = [] - for tag, query in iteritems(criteria): - rsl.append(query == self.get_value(tag)) - return all(rsl) - - - def _isIn(self, criteria): - rsl = [] - for tag, query in iteritems(criteria): - if isinstance(query, list): - for q in query: - rsl.append(q in self.get_value(tag)) - else: - rsl.append(query in self.get_value(tag)) - return all(rsl) - - - def get_value(self, tag): - if tag == "dicomPath": - return self.dicomPath - elif tag in self.ds: - return self.ds.data_element(tag).value - else: - return None - diff --git a/dcm2bids/sidecarparser.py b/dcm2bids/sidecarparser.py new file mode 100644 index 00000000..c55a7137 --- /dev/null +++ b/dcm2bids/sidecarparser.py @@ -0,0 +1,123 @@ +# -*- coding: utf-8 -*- + + +import itertools +import os +from collections import defaultdict, OrderedDict +from future.utils import iteritems +from .structure import Acquisition +from .utils import load_json, splitext_ + + +class Sidecarparser(object): + + def __init__(self, sidecars, descriptions): + self.sidecars = sidecars + self.descriptions = descriptions + self.graph = self._generateGraph() + self.acquisitions = self._generateAcquisitions() + self.findRuns() + + + def _generateGraph(self): + graph = OrderedDict((_, []) for _ in self.sidecars) + for sidecar, index in itertools.product( + self.sidecars, range(len(self.descriptions))): + self._sidecar = load_json(sidecar) + if self._respect(self.descriptions[index]["criteria"]): + graph[sidecar].append(index) + return graph + + + def _generateAcquisitions(self): + rsl = [] + print("") + for sidecar, match_descs in iteritems(self.graph): + base = splitext_(sidecar)[0] + basename = os.path.basename(sidecar) + if len(match_descs) == 1: + print("'{}' satisfies one description".format(basename)) + acq = self._acquisition( + base, self.descriptions[match_descs[0]]) + rsl.append(acq) + elif len(match_descs) == 0: + print("'{}' satisfies no description".format(basename)) + else: + print("'{}' satisfies several descriptions".format(basename)) + return rsl + + + def findRuns(self): + def list_duplicates(seq): + """ + http://stackoverflow.com/a/5419576 + """ + tally = defaultdict(list) + for i, item in enumerate(seq): + tally[item].append(i) + return ((key,locs) for key,locs in tally.items() if len(locs)>1) + + suffixes = [_.suffix for _ in self.acquisitions] + for suffix, dup in sorted(list_duplicates(suffixes)): + print("'{}': has several runs".format(suffix)) + for run, acq_index in enumerate(dup): + runStr = "run-{:02d}".format(run+1) + acq = self.acquisitions[acq_index] + if acq.customLabels is None: + acq.customLabels = runStr + else: + acq.customLabels += "_" + runStr + print("") + + + def _acquisition(self, base, desc): + acq = Acquisition(base, desc["dataType"], desc["suffix"]) + if "customLabels" in desc: + acq.customLabels = desc["customLabels"] + else: + acq.customLabels = None + return acq + + + def _respect(self, criteria): + isEqual = "equal" in criteria + isIn = "in" in criteria + + # Check if there is some criteria + if not any([isEqual, isIn]): + return False + + if isEqual: + rsl_equal = self._isEqual(criteria["equal"]) + else: + rsl_equal = True + + if isIn: + rsl_in = self._isIn(criteria["in"]) + else: + rsl_in = True + + return all([rsl_equal, rsl_in]) + + + def _isEqual(self, criteria): + rsl = [] + for tag, query in iteritems(criteria): + rsl.append(query == self.get_value(tag)) + return all(rsl) + + + def _isIn(self, criteria): + rsl = [] + for tag, query in iteritems(criteria): + if isinstance(query, list): + for q in query: + rsl.append(q in self.get_value(tag)) + else: + rsl.append(query in self.get_value(tag)) + return all(rsl) + + + def get_value(self, tag): + return self._sidecar[tag] + diff --git a/dcm2bids/structure.py b/dcm2bids/structure.py index 57654ea9..05957341 100644 --- a/dcm2bids/structure.py +++ b/dcm2bids/structure.py @@ -55,8 +55,8 @@ class Acquisition(object): """ """ - def __init__(self, dicomPath, dataType, suffix, customLabels=None): - self.dicomPath = dicomPath + def __init__(self, base, dataType, suffix, customLabels=None): + self.base = base self.dataType = dataType self._suffix = suffix self.customLabels = customLabels diff --git a/dcm2bids/utils.py b/dcm2bids/utils.py new file mode 100644 index 00000000..f06fe182 --- /dev/null +++ b/dcm2bids/utils.py @@ -0,0 +1,34 @@ +# -*- coding: utf-8 -*- + + +import json +import os +import shutil + + +def load_json(filename): + with open(filename, 'r') as f: + data = json.load(f) + return data + + +def make_directory_tree(directory): + if not os.path.exists(directory): + os.makedirs(directory) + + +def clean(directory): + make_directory_tree(directory) + if not os.listdir(directory) == []: + shutil.rmtree(directory) + make_directory_tree(directory) + else: + make_directory_tree(directory) + + +def splitext_(path): + for ext in ['.nii.gz']: + if path.endswith(ext): + return path[:-len(ext)], path[-len(ext):] + return os.path.splitext(path) + diff --git a/environment.yml b/environment.yml index 9f7a72be..5e28bb35 100644 --- a/environment.yml +++ b/environment.yml @@ -1,5 +1,3 @@ name: dcm2bids dependencies: - future - - pydicom - - pyyaml diff --git a/example/config.json b/example/config.json index f77afb03..ff18d24a 100644 --- a/example/config.json +++ b/example/config.json @@ -1,71 +1,55 @@ { - "dcm2bids_options":{ - "force": false - }, - "batch_options": { - "isGz": true, - "isFlipY": false, - "isVerbose": false, - "isCreateBIDS": true, - "isOnlySingleFile": false - }, "descriptions": [ { "dataType": "anat", "suffix": "T1w", "criteria": { - "is": { - "SeriesDescription": "MPRAGE" - } + "in": {"SeriesDescription": "T1W_3D"} } }, { "dataType": "anat", - "suffix": "FLAIR", + "suffix": "T2w", "criteria": { - "in": { - "SeriesDescription": "FLAIR" - } + "in": {"SeriesDescription": "TSE"}, + "equal": {"EchoTime": 0.1} } }, { "dataType": "anat", - "suffix": "T2w", + "suffix": "PD", + "criteria": { + "in": {"SeriesDescription": "TSE"}, + "equal": {"EchoTime": 0.008} + } + }, + { + "dataType": "anat", + "suffix": "FLAIR", "criteria": { - "in": { - "SeriesDescription": "T2" - } + "in": {"SeriesDescription": "FLAIR"} } }, { "dataType": "dwi", "suffix": "dwi", "criteria": { - "in": { - "ImageType": ["DIFFUSION", "MOSAIC"] - } + "in": {"SeriesDescription": "DWI"} } }, { - "dataType": "fmap", - "suffix": "epi", - "customLabels": "dir-pa", + "dataType": "anat", + "suffix": "SWI", "criteria": { - "in": { - "ImageType": "DIFFUSION", - "SeriesDescription": "ep2d_diff_PA" - } + "in": {"SeriesDescription": "SWI"} } }, { - "dataType": "fmap", - "suffix": "epi", - "customLabels": "dir-ap", + "dataType": "func", + "suffix": "bold", + "customLabels": "task-rest", "criteria": { - "in": { - "ImageType": "DIFFUSION", - "SeriesDescription": "ep2d_diff_AP" - } + "equal": {"SeriesDescription": "rs_fMRI"} } } ] diff --git a/scripts/dcm2bids b/scripts/dcm2bids index 94e9f1a3..502e72f6 100755 --- a/scripts/dcm2bids +++ b/scripts/dcm2bids @@ -3,7 +3,6 @@ import argparse -import os import sys from dcm2bids.dcm2bids import Dcm2bids @@ -16,12 +15,6 @@ def get_arguments(): Documentation at https://github.com/cbedetti/Dcm2Bids """) - parser.add_argument( - "-o", "--bids_dir", - required=True, - help="BIDS directory output", - ) - parser.add_argument( "-d", "--dicom_dir", required=True, @@ -47,10 +40,10 @@ def get_arguments(): ) parser.add_argument( - "-n", - "--dryrun", + "-y", + "--yes", required=False, action='store_true', - help="Do not launch dcm2niibatch", + help="Always reply yes to continue", ) args = parser.parse_args() @@ -60,7 +53,6 @@ def get_arguments(): def main(): """Let's go""" args = get_arguments() - app = Dcm2bids(**vars(args)) return app.run() diff --git a/scripts/dcm2bidsbatch b/scripts/dcm2bids_helper similarity index 60% rename from scripts/dcm2bidsbatch rename to scripts/dcm2bids_helper index eec9af00..9e80c102 100755 --- a/scripts/dcm2bidsbatch +++ b/scripts/dcm2bids_helper @@ -4,25 +4,22 @@ import argparse import sys +from dcm2bids.dcm2niix import Dcm2niix def get_arguments(): parser = argparse.ArgumentParser( formatter_class=argparse.RawDescriptionHelpFormatter, - description=""" - """, + description="", epilog=""" - - Not Implemented - + Documentation at https://github.com/cbedetti/Dcm2Bids """) - ''' parser.add_argument( - "yaml", required=True, nargs='?', - help="YAML file describing your dicom", + "-d", "--dicom_dir", + required=True, + help="DICOM files directory", ) - ''' args = parser.parse_args() return args @@ -31,12 +28,8 @@ def get_arguments(): def main(): """Let's go""" args = get_arguments() - - #print args - #cmd = "dcm2bids -o {} -d {} -p {}".format - #print cmd - - return 0 + app = Dcm2niix(**vars(args)) + return app.run() if __name__ == '__main__':