Merge pull request #33 from AdebayoBraimah/dev5

Dev5

CHANGES.rst

@@ -1,6 +1,20 @@
 CHANGES
 =========
 
+0.2.0a0
+---------
+
+This version is an alpha release that contains a bug fix, and substantial improvements and updates.
+
+* BUG FIX: Fixed bug in which a DICOM file of the same series would be converted as separate acquisitions.
+* UPDATE: Writes BIDS directory related files, such as the: ``README``, ``dataset_description.json``, and ``.bidsignore`` files.
+* UPDATE: Optionally writes the ``participants.tsv`` and each subject's ``scans.tsv``.
+* UPDATE: Utilizes a database to keep track of which source files have already been processed to avoid converting data that has already been processed.
+* UPDATE: New functionality that symbolically links each subject's directory to the desired directory structure that ``convert_source`` requires.
+  * This allows for mapping a subject's study ID to their BIDS subject ID if these are different.
+* UPDATE: Added wait bar to command line interface.
+* UPDATE: Added function and executable to rename unknown scans.
+
 v0.1.1
 ---------
 

convert_source/__init__.py

@@ -1,25 +1,17 @@
 # -*- coding: utf-8 -*-
 """Python package used for the conversion of source DICOM, PAR REC, or NIFTI data to raw BIDS NIFTI data.
 """
-
-name: str = "convert_source"
-
-import pathlib
-import sys
 import os
 
-_pkg_path: str = str(pathlib.Path(os.path.abspath(__file__)).parents[1])
-sys.path.append(_pkg_path)
-_version_file: str = os.path.abspath(
-    os.path.join(
-        os.path.dirname(__file__),
-        "version.txt"
-        )
-)
+name: str = "convert_source"
+_version_file: str = os.path.abspath(os.path.join(os.path.dirname(__file__),"version.txt"))
 
-from convert_source.cs_utils.utils import file_to_screen
+with open(_version_file,"r") as f:
+    file_contents: str = f.read()
+    _cs_version: str = file_contents.strip("\n")
+    f.close()
 
-# More on organizing author information:
+# More information about organizing author information:
 # https://stackoverflow.com/questions/1523427/what-is-the-common-header-format-of-python-files
 # http://epydoc.sourceforge.net/manual-fields.html#module-metadata-variables
 
@@ -29,7 +21,7 @@
                "Imaging Research Center", 
                "CCHMC Dept. of Radiology"]
 __license__ = "GPL"
-__version__ = file_to_screen(_version_file)
+__version__ = _cs_version
 __maintainer__ = "Adebayo Braimah"
 __email__ = "adebayo.braimah@gmail.com"
 __status__ = "Development"