Windows file paths

[kousu]

dcm2bids crashes if given filepaths with backslashes in it. They get erased.

Reproduction

On Windows, I installed from master

C:\Users\user\src\Dcm2bids>git branch --show-current
master
C:\Users\user\src\Dcm2bids>pip install -e .
Obtaining file:///C:/Users/user/src/Dcm2bids
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: future>=0.17.1 in c:\users\user\appdata\local\programs\python\python38-32\lib\site-packages (from dcm2bids==2.1.4) (0.18.2)
Installing collected packages: dcm2bids
  Found existing installation: dcm2bids 2.1.4
    Uninstalling dcm2bids-2.1.4:
      Successfully uninstalled dcm2bids-2.1.4
  Running setup.py develop for dcm2bids
Successfully installed dcm2bids
WARNING: You are using pip version 19.2.3, however version 20.1.1 is available.
You should consider upgrading via the 'python -m pip install --upgrade pip' command.

C:\Users\user\src\Dcm2bids>dcm2bids
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR] [--forceDcm2niix] [--clobber]
                [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
dcm2bids: error: the following arguments are required: -d/--dicom_dir, -p/--participant, -c/--config

(I'm surprised pip install -e . worked, where python setup.py install didn't ?? #76)

Get this testing dataset:

C:\Users\user\src\Dcm2bids>curl -JLO "https://osf.io/7d2j5/?action=download&version=3"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   469  100   469    0     0    469      0  0:00:01 --:--:--  0:00:01  1155
100 14.2M  100 14.2M    0     0  2434k      0  0:00:06  0:00:06 --:--:-- 3135k
curl: Saved to filename 'data_testing.zip'

C:\Users\user\src\Dcm2bids>rem And then manually extract data_testing.zip using the Windows GUI.

Then try to run it:

C:\Users\user\src\Dcm2bids>mkdir output

C:\Users\user\src\Dcm2bids>dcm2bids -d data_testing\data_testing\dicom_unsorted -o output -p "" -c example\config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.18362-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.8.3 (tags/v3.8.3:6f8c832, May 13 2020, 22:20:19) [MSC v.1925 32 bit (Intel)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20200331
INFO:dcm2bids.dcm2bids:participant: sub-
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\user\src\Dcm2bids\example\config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\user\src\Dcm2bids\output
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o output\tmp_dcm2bids\sub- data_testing\data_testing\dicom_unsorted
Error: Input folder invalid: data_testingdata_testingdicom_unsorted
Traceback (most recent call last):
  File "C:\Users\user\AppData\Local\Programs\Python\Python38-32\Scripts\dcm2bids-script.py", line 11, in <module>
    load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')()
  File "c:\users\user\src\dcm2bids\dcm2bids\dcm2bids.py", line 290, in main
    return app.run()
  File "c:\users\user\src\dcm2bids\dcm2bids\dcm2bids.py", line 120, in run
    dcm2niix.run(self.forceDcm2niix)
  File "c:\users\user\src\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\user\src\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\user\src\dcm2bids\dcm2bids\utils.py", line 112, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "c:\users\user\appdata\local\programs\python\python38-32\lib\subprocess.py", line 411, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "c:\users\user\appdata\local\programs\python\python38-32\lib\subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'outputtmp_dcm2bidssub-', 'data_testingdata_testingdicom_unsorted']' returned non-zero exit status 5.