Merge pull request #24 from AdebayoBraimah/dev5

Dev5

Author: AdebayoBraimah

.gitignore

@@ -8,7 +8,8 @@ convert_source/*.ipynb
 tests/img.test.dir/*
 .vscode/*
 test.data/*
-deploy/*
+
+# deploy/*
 
 # Command to file al .DS_STOREs files:
 # find . -name ".DS_Store"

.readthedocs.yml

@@ -0,0 +1,7 @@
+version: 2
+
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt
+    - requirements: requirements.txt

CHANGES.rst

@@ -1,13 +1,19 @@
 CHANGES
 =========
 
+v0.1.0
+---------
+
+* BUG FIX: Fixed bug in setup, which prevented proper installation and usage of the ``study_proc`` executable.
+* UPDATE: The documentation is now `available <https://convert-source.readthedocs.io/en/master/>`_.
+
 v0.1.rc1
 ---------
 
 * Includes ``setup.py`` file, in addition to be published on PyPI.
 * Much improved documentation.
 
-v0.1.rc1alpha
+v0.1.rc1a
 --------------
 
 Version: ``0.1 - release candidate 1 - alpha``

MANIFEST.in

@@ -1,4 +1,6 @@
 # Misc
 include LICENSE
 include CHANGES.rst
+include convert_source/version.txt
+include convert_source/config/*
 exclude .circleci/config.yml

README.md

@@ -1,4 +1,4 @@
-[![CircleCI](https://circleci.com/gh/AdebayoBraimah/convert_source.svg?style=svg)](https://app.circleci.com/pipelines/github/AdebayoBraimah/convert_source)
+[![CircleCI](https://circleci.com/gh/AdebayoBraimah/convert_source.svg?style=svg)](https://app.circleci.com/pipelines/github/AdebayoBraimah/convert_source) [![Documentation Status](https://readthedocs.org/projects/convert-source/badge/?version=latest)](https://convert-source.readthedocs.io/en/latest/?badge=latest)
 
 # convert_source
 Convert source `DICOM`, `PAR REC` or `NIFTI` image data to BIDS directory layout.

convert_source/__init__.py

@@ -10,7 +10,12 @@
 
 _pkg_path: str = str(pathlib.Path(os.path.abspath(__file__)).parents[1])
 sys.path.append(_pkg_path)
-_version_file: str = os.path.abspath("version.txt")
+_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
 

convert_source/batch_convert.py

@@ -3,8 +3,8 @@
 """
 
 # TODO:
-#   * [PENDING] Figure out where tmp directory path is being printed.
-#       * See functions that use TmpDir class's rm_tmp_dir() function
+#   * Add option for renaming identified unknown files
+#   * Add file search for image files with no extensions (DICOMs)
 #   * Add doc building to CI workflow.
 #   * Replace triple single quotes (''') with triple double quotes (""")
 
@@ -904,7 +904,7 @@ def source_to_bids(sub_data: SubDataInfo,
                                            append_dwi_info=append_dwi_info,
                                            zero_pad=zero_pad,
                                            cprss_lvl=cprss_lvl)
-                    tmp.rm_tmp_dir()
+                    _ = tmp.rm_tmp_dir()
                     return (imgs,
                             jsons,
                             bvals,
@@ -929,7 +929,7 @@ def source_to_bids(sub_data: SubDataInfo,
                                            append_dwi_info=append_dwi_info,
                                            zero_pad=zero_pad,
                                            cprss_lvl=cprss_lvl)
-                    tmp.rm_tmp_dir()
+                    _ = tmp.rm_tmp_dir()
                     return (imgs,
                             jsons,
                             bvals,
@@ -991,13 +991,13 @@ def source_to_bids(sub_data: SubDataInfo,
                     else:
                         bvecs.append("")
                 # Clean-up
-                tmp.rm_tmp_dir()
+                _ = tmp.rm_tmp_dir()
                 return (imgs,
                         jsons,
                         bvals,
                         bvecs)
             except ConversionError:
-                tmp.rm_tmp_dir()
+                _ = tmp.rm_tmp_dir()
                 return [""],[""],[""],[""]
 
 def nifti_to_bids(sub_data: SubDataInfo,
@@ -1075,7 +1075,7 @@ def nifti_to_bids(sub_data: SubDataInfo,
 
     # Use TmpDir and NiiFile class context managers
     with TmpDir(tmp_dir=sub_tmp, use_cwd=False) as tmp:
-        tmp.mk_tmp_dir()
+        _ = tmp.mk_tmp_dir()
         with NiiFile(data) as n:
             [path, basename, ext] = n.file_parts()
             img_files: List[str] = glob.glob(os.path.join(path,basename + "*" + ext))
@@ -1129,7 +1129,11 @@ def nifti_to_bids(sub_data: SubDataInfo,
                 elif (not img_data.jsons[i]) and (i == 0):
                     json_dict: Dict = read_json(json_file="")
 
+                    param_dict: Dict = get_data_params(file=data,
+                                                    json_file=img_data.jsons[i])
+
                     metadata: Dict = dict_multi_update(dictionary=None, **meta_dict)
+                    metadata: Dict = dict_multi_update(dictionary=metadata, **param_dict)
                     metadata: Dict = dict_multi_update(dictionary=metadata, **mod_dict)
 
                     bids_dict: Dict = construct_bids_dict(meta_dict=metadata,
@@ -1266,7 +1270,7 @@ def nifti_to_bids(sub_data: SubDataInfo,
                     bvals.append("")
                     bvecs.append("")
         # Clean-up
-        tmp.rm_tmp_dir()
+        _ = tmp.rm_tmp_dir()
 
         return (imgs,
                 jsons,
@@ -1398,7 +1402,7 @@ def bids_ignore(out_dir: str) -> str:
     # Write to file using File class context manager
     with File(new_file) as f:
         f.write_txt(".misc \n")
-        f.write_txt("unknown \n")
+        f.write_txt("unknown/* \n")
 
     return new_file