Dev 0.5.0

README.md

@@ -4,65 +4,40 @@ 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
 ```
 
 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-<PARTICIPANT>` 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

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
+

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)
+