Merge pull request #210 from SamGuay/improve_helper

[FIX,ENH] - Improve dcm2bids_helper mod

dcm2bids/cli/dcm2bids.py

@@ -49,7 +49,7 @@ def _build_arg_parser():
                         " will check if your output folder is BIDS valid. [%(default)s]\n"
                         f"bids-validator needs to be installed check: {DEFAULT.link_bids_validator}")
 
-    p.add_argument("--forceDcm2niix",
+    p.add_argument("--force_dcm2niix",
                    action="store_true",
                    help="Overwrite previous temporary dcm2niix "
                         "output if it exists.")

dcm2bids/cli/dcm2bids_helper.py

@@ -1,13 +1,19 @@
 # -*- coding: utf-8 -*-
 
-"""helper module"""
-
+"""
+Converts DICOM files to NIfTI files including their JSON sidecars in a
+temporary directory which can be inspected to make a dc2mbids config file.
+"""
+import logging
 import argparse
-from os.path import join as opj
-
+import sys
+import os
+from pathlib import Path
+from datetime import datetime
 from dcm2bids.dcm2niix_gen import Dcm2niixGen
 from dcm2bids.utils.args import assert_dirs_empty
 from dcm2bids.utils.utils import DEFAULT
+from dcm2bids.utils.logger import setup_logging
 
 
 def _build_arg_parser():
@@ -19,11 +25,20 @@ def _build_arg_parser():
                    help="DICOM files directory.")
 
     p.add_argument("-o", "--output_dir",
-                   required=False, default=DEFAULT.cliOutputDir,
-                   help="Output BIDS directory."
-                        " (Default: %(default)s)")
-
-    p.add_argument('--force',
+                   required=False,
+                   default=Path(DEFAULT.cliOutputDir) / DEFAULT.tmpDirName /
+                   DEFAULT.helperDir,
+                   help="Output directory. (Default: [%(default)s]")
+
+    p.add_argument("-n", "--nest",
+                   nargs="?", const=True, default=False, required=False,
+                   help="Nest a directory in <output_dir>. Useful if many helper "
+                        "runs are needed\nto make a config file due to slight "
+                        "variations in MRI acquisitions.\n"
+                        "Defaults to DICOM_DIR if no name is provided.\n"
+                        "(Default: [%(default)s])")
+
+    p.add_argument('--force', '--force_dcm2niix',
                    dest='overwrite', action='store_true',
                    help='Force command to overwrite existing output files.')
 
@@ -34,14 +49,36 @@ def main():
     """Let's go"""
     parser = _build_arg_parser()
     args = parser.parse_args()
-
-    out_folder = opj(args.output_dir, 'tmp_dcm2bids', 'helper')
-    assert_dirs_empty(parser, args, out_folder)
-
-    app = Dcm2niixGen(dicomDirs=args.dicom_dir, bidsDir=args.output_dir)
-    rsl = app.run()
-    print("Example in:")
-    print(opj(args.output_dir, DEFAULT.tmpDirName, DEFAULT.helperDir))
+    out_dir = Path(args.output_dir)
+    log_path = (Path(DEFAULT.cliOutputDir)
+                / DEFAULT.tmpDirName
+                / "log"
+                / f"helper_{datetime.now().isoformat().replace(':', '')}.log")
+    if args.nest:
+        if isinstance(args.nest, str):
+            log_path = Path(
+              str(log_path).replace("helper_",
+                                    f"helper_{args.nest.replace(os.path.sep, '-')}_"))
+            out_dir = out_dir / args.nest
+        else:
+            log_path = Path(str(log_path).replace(
+              "helper_", f"helper_{args.dicom_dir[0].replace(os.path.sep, '-')}_")
+                            )
+            out_dir = out_dir / args.dicom_dir[0]
+
+    log_path.parent.mkdir(parents=True, exist_ok=True)
+    setup_logging("info", log_path)
+    logger = logging.getLogger(__name__)
+
+    logger.info("Running the following command: \n" + " ".join(sys.argv) + "\n")
+
+    assert_dirs_empty(parser, args, out_dir)
+
+    app = Dcm2niixGen(dicomDirs=args.dicom_dir, bidsDir=out_dir, helper=True)
+
+    rsl = app.run(force=args.overwrite)
+    logger.info(f"Helper files in: {out_dir}\n")
+    logger.info(f"Log file saved at {log_path}")
 
     return rsl
 

dcm2bids/dcm2bids_gen.py

@@ -32,7 +32,7 @@ class Dcm2BidsGen(object):
         output_dir (path): Path to the BIDS base folder
         session (str): Optional label of a session
         clobber (boolean): Overwrite file if already in BIDS folder
-        forceDcm2niix (boolean): Forces a cleaning of a previous execution of
+        force_dcm2niix (boolean): Forces a cleaning of a previous execution of
                                  dcm2niix
         log_level (str): logging level
     """
@@ -47,7 +47,7 @@ def __init__(
         auto_extract_entities=DEFAULT.auto_extract_entities,
         session=DEFAULT.session,
         clobber=DEFAULT.clobber,
-        forceDcm2niix=DEFAULT.forceDcm2niix,
+        force_dcm2niix=DEFAULT.force_dcm2niix,
         log_level=DEFAULT.logLevel,
         **_
     ):
@@ -60,7 +60,7 @@ def __init__(
         self.clobber = clobber
         self.bids_validate = bids_validate
         self.auto_extract_entities = auto_extract_entities
-        self.forceDcm2niix = forceDcm2niix
+        self.force_dcm2niix = force_dcm2niix
         self.logLevel = log_level
 
         # logging setup
@@ -113,7 +113,7 @@ def run(self):
         check_latest()
         check_latest("dcm2niix")
 
-        dcm2niix.run(self.forceDcm2niix)
+        dcm2niix.run(self.force_dcm2niix)
 
         sidecars = []
         for filename in dcm2niix.sidecarFiles:

dcm2bids/dcm2niix_gen.py

@@ -25,16 +25,20 @@ class Dcm2niixGen(object):
     """
 
     def __init__(
-        self, dicomDirs, bidsDir, participant=None, options=DEFAULT.dcm2niixOptions
+        self,
+        dicomDirs,
+        bidsDir,
+        participant=None,
+        options=DEFAULT.dcm2niixOptions,
+        helper=False
     ):
         self.logger = logging.getLogger(__name__)
-
         self.sidecarsFiles = []
-
         self.dicomDirs = dicomDirs
         self.bidsDir = bidsDir
         self.participant = participant
         self.options = options
+        self.helper = helper
 
     @property
     def outputDir(self):
@@ -43,10 +47,12 @@ def outputDir(self):
             A directory to save all the output files of dcm2niix
         """
         tmpDir = self.participant.prefix if self.participant else DEFAULT.helperDir
+        tmpDir = self.bidsDir / DEFAULT.tmpDirName / tmpDir
+        if self.helper:
+            tmpDir = self.bidsDir
+        return tmpDir
 
-        return self.bidsDir / DEFAULT.tmpDirName / tmpDir
-
-    def run(self, force=False):
+    def run(self, force=False, helper=False):
         """ Run dcm2niix if necessary
 
         Args:
@@ -58,7 +64,7 @@ def run(self, force=False):
         """
         try:
             oldOutput = os.listdir(self.outputDir) != []
-        except:
+        except Exception:
             oldOutput = False
 
         if oldOutput and force:
@@ -69,8 +75,6 @@ def run(self, force=False):
 
             shutil.rmtree(self.outputDir, ignore_errors=True)
 
-            # os.makedirs(self.outputDir, exist_ok=True)
-            # python2 compatibility
             if not os.path.exists(self.outputDir):
                 os.makedirs(self.outputDir)
 
@@ -79,11 +83,9 @@ def run(self, force=False):
         elif oldOutput:
             self.logger.warning("Previous dcm2niix directory output found:")
             self.logger.warning(self.outputDir)
-            self.logger.warning("Use --forceDcm2niix to rerun dcm2niix")
+            self.logger.warning("Use --force_dcm2niix to rerun dcm2niix \n")
 
         else:
-            # os.makedirs(self.outputDir, exist_ok=True)
-            # python2 compatibility
             if not os.path.exists(self.outputDir):
                 os.makedirs(self.outputDir)
 
@@ -101,7 +103,7 @@ def execute(self):
 
             try:
                 output = output.decode()
-            except:
+            except Exception:
                 pass
 
             self.logger.debug("\n%s", output)

dcm2bids/utils/args.py

@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 
-import os
 import shutil
+from pathlib import Path
+import os
 
 
 def assert_dirs_empty(parser, args, required):
@@ -18,30 +19,22 @@ def assert_dirs_empty(parser, args, required):
     required: string or list of paths to files
         Required paths to be checked.
     """
-    def check(path):
-        if os.path.isdir(path):
-            if os.listdir(path):
+    def check(path: Path):
+        if path.is_dir():
+            if any(path.iterdir()):
                 if not args.overwrite:
                     parser.error(
-                        f"Output directory {path} isn't empty, so some files "
-                        "could be overwritten or deleted.\nRerun the command"
-                        " with --force option to overwrite "
+                        f"Output directory {path}{os.sep} isn't empty, so some files "
+                        "could be overwritten or deleted.\nRerun the command "
+                        "with --force option to overwrite "
                         "existing output files.")
             else:
-                for the_file in os.listdir(path):
-                    file_path = os.path.join(path, the_file)
-                    try:
-                        if os.path.isfile(file_path):
-                            os.unlink(file_path)
-                        elif os.path.isdir(file_path):
-                            shutil.rmtree(file_path)
-                    except Exception as e:
-                        print(e)
+                shutil.rmtree(path)
 
     if isinstance(required, str):
-        required = [required]
+        required = Path(required)
 
-    for cur_dir in required:
+    for cur_dir in [required]:
         check(cur_dir)
 
 

dcm2bids/utils/utils.py

@@ -27,7 +27,7 @@ class DEFAULT(object):
     bids_validate = False
     auto_extract_entities = False
     clobber = False
-    forceDcm2niix = False
+    force_dcm2niix = False
     defaceTpl = None
     logLevel = "WARNING"