Merge pull request #40 from AdebayoBraimah/dev5

Dev5
AdebayoBraimah · Jun 24, 2021 · 2edd798 · 2edd798
2 parents a1e61fe + 6f210b7
commit 2edd798
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,6 +1,16 @@
 CHANGES
 =========
 
+0.2.0a8
+---------
+
+This version is an alpha release that contains several bug fixes and updates.
+
+* BUG FIX: Fixed bug in which an unexpected parent DICOM directory could throw errors.
+* BUG FIX: Fixed bug in which BIDS related parameters were not added to the output file name.
+* UPDATE: More robust and reliable BIDS file naming.
+* ENHANCEMENT: Added support for native symbolic linking.
+
 0.2.0a7
 ---------
 

diff --git a/convert_source/__init__.py b/convert_source/__init__.py
@@ -12,16 +12,16 @@
     f.close()
 
 # 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
+#   * https://stackoverflow.com/questions/1523427/what-is-the-common-header-format-of-python-files
+#   * http://epydoc.sourceforge.net/manual-fields.html#module-metadata-variables
 
-__author__ = "Adebayo Braimah"
-__credits__ = ["Adebayo Braimah",
-               "Cincinnati Children's Hospital Medical Center", 
-               "Imaging Research Center", 
-               "CCHMC Dept. of Radiology"]
-__license__ = "GPL"
-__version__ = _cs_version
-__maintainer__ = "Adebayo Braimah"
-__email__ = "adebayo.braimah@gmail.com"
-__status__ = "Development"
+__author__          = "Adebayo Braimah"
+__credits__         = ["Adebayo Braimah",
+                       "Cincinnati Children's Hospital Medical Center", 
+                       "Imaging Research Center", 
+                       "CCHMC Dept. of Radiology"]
+__license__         = "GPL"
+__version__         = _cs_version
+__maintainer__      = "Adebayo Braimah"
+__email__           = "adebayo.braimah@gmail.com"
+__status__          = "Development"
diff --git a/convert_source/batch_convert.py b/convert_source/batch_convert.py
@@ -712,7 +712,7 @@ def _get_bids_name_args(bids_name_dict: Dict,
     case4: bool = False
 
     params_var: List[str] = [task, acq, ce, acq_dir, rec, echo, case1, mag2, case2, case3, case4]
-    params_str: List[str] = ["task", "acq", "ce", "acq_dir", "rec", "echo", "case1", "mag2", "case2", "case3", "case4"]
+    params_str: List[str] = ["task", "acq", "ce", "dir", "rec", "echo", "case1", "mag2", "case2", "case3", "case4"]
 
     if len(params_str) == len(params_var):
         pass

diff --git a/convert_source/batch_symlink.py b/convert_source/batch_symlink.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Command line wrapper for `convert_source`'s study directory symlink functions. 
+"""Command line wrapper for ``convert_source``'s study directory symlink functions. 
    Performs symlinking for a study's subject imaging data.
 """
 import pathlib
@@ -14,13 +14,14 @@
 )
 
 _pkg_path: str = str(
-    pathlib.Path(
-        os.path.abspath(__file__)
-            ).parents[2])
+                    pathlib.Path(
+                        os.path.abspath(__file__)
+                            ).parents[2])
 
 sys.path.append(_pkg_path)
 
 from convert_source.cs_utils.fileio import LogFile
+from convert_source.cs_utils.utils import sym_link
 
 link_version = '0.0.1'
 
@@ -106,6 +107,8 @@ def create_study_sym_links(study_dir: str,
                            infile: str,
                            mapfile: str,
                            outdir: str,
+                           native: Optional[bool] = True,
+                           overwrite: Optional[bool] = False,
                            log_file: Optional[LogFile] = None
                           ) -> List[str]:
     """Creates another study directory of sym-linked subject directories to the original study directory.
@@ -124,13 +127,15 @@ def create_study_sym_links(study_dir: str,
         infile: Input file of directories to be mapped.
         mapfile: Corresponding file that contains the subject directories to be mapped to.
         outdir: Output directory for all symlinked directories.
+        native: Use native UNIX linking tool instead of python's symbolic linking tool.
+        overwrite: Overwrite symbolic link if it already exists.
         log_file: LogFile object for logging.
     
     Returns:
         List of sym-linked directories.
         
     Raises:
-        IndexError is raised if the number of entries in ``infile`` and ``mapfile`` are not equal.
+        IndexError: Raised if the number of entries in ``infile`` and ``mapfile`` are not equal.
     """
     study_dir: str = os.path.abspath(study_dir)
 
@@ -165,7 +170,10 @@ def create_study_sym_links(study_dir: str,
         sub_dir: str = os.path.join(study_dir,i)
         tar_dir: str = os.path.join(outdir,j)
 
-        if os.path.exists(tar_dir) and os.path.islink(tar_dir):
+        if os.path.exists(tar_dir) and os.path.islink(tar_dir) and overwrite:
+            if log_file:
+                log_file.log(f"(Symbolically linked) directory has been overwritten, linking the following: {i} -> {j}.")
+        elif os.path.exists(tar_dir) and os.path.islink(tar_dir):
             if log_file:
                 log_file.log(f"(Symbolically linked) directory already exists: {i} -> {j}.")
         elif os.path.exists(tar_dir):
@@ -174,7 +182,9 @@ def create_study_sym_links(study_dir: str,
         else:
             if log_file:
                 log_file.log(f"Symbollically linked directories: {i} -> {j}.")
-            os.symlink(sub_dir,tar_dir)
+            sym_link(src=sub_dir,
+                     tar=tar_dir,
+                     native=native)
         dir_list.append(tar_dir)
     return dir_list
 

diff --git a/convert_source/cs_utils/bids_info.py b/convert_source/cs_utils/bids_info.py
@@ -503,30 +503,35 @@ def search_bids(s: str,
             bids_name_dict[modality_type]['modality_label'] = modality_label
         return bids_name_dict
 
-    # Use dict.get method here
     if depth(bids_search[modality_type]) == 3:
-        try:
-            for (k1,v1),(k2,v2) in zip(bids_search[modality_type][modality_label].items(),bids_map[modality_type][modality_label].items()):
-                    for va,vb in zip(v1,v2):
-                        if list_in_substr(in_list=[va],in_str=s):
-                            bids_name_dict[modality_type]['modality_label'] = modality_label
-                            bids_name_dict[modality_type][k1] = vb
-                        else:
-                            bids_name_dict[modality_type]['modality_label'] = modality_label
-        except (TypeError,KeyError):
-            pass
+        for (k1,v1),(k2,v2) in zip(bids_search[modality_type].get(modality_label,'').items(),bids_map[modality_type].get(modality_label,'').items()):
+            if (v1 is None) and (v2 is None):
+                continue
+            elif (v1 is None) and v2:
+                bids_name_dict[modality_type]['modality_label'] = modality_label
+                bids_name_dict[modality_type][k1] = ''.join(v2)
+            else:
+                for va,vb in zip(v1,v2):
+                    if list_in_substr(in_list=[va],in_str=s):
+                        bids_name_dict[modality_type]['modality_label'] = modality_label
+                        bids_name_dict[modality_type][k1] = vb
+                    else:
+                        bids_name_dict[modality_type]['modality_label'] = modality_label                        
     elif depth(bids_search[modality_type]) == 4:
-        try:
-            for (k1,v1),(k2,v2) in zip(bids_search[modality_type][modality_label][task].items(),bids_map[modality_type][modality_label][task].items()):
-                    for (va,vb) in zip(v1,v2):
-                        if list_in_substr(in_list=[va],in_str=s):
-                            bids_name_dict[modality_type]['modality_label'] = modality_label
-                            bids_name_dict[modality_type]['task'] = task
-                            bids_name_dict[modality_type][k1] = vb
-                        else:
-                            bids_name_dict[modality_type]['modality_label'] = modality_label
-                            bids_name_dict[modality_type]['task'] = task
-        except (TypeError,KeyError):
-            pass
-
+        for (k1,v1),(k2,v2) in zip(bids_search[modality_type].get(modality_label,'').get(task,'').items(),bids_map[modality_type].get(modality_label,'').get(task,'').items()):
+            if (v1 is None) and (v2 is None):
+                continue
+            elif (v1 is None) and v2:
+                bids_name_dict[modality_type]['modality_label'] = modality_label
+                bids_name_dict[modality_type]['task'] = task
+                bids_name_dict[modality_type][k1] = ''.join(v2)
+            else:
+                for (va,vb) in zip(v1,v2):
+                    if list_in_substr(in_list=[va],in_str=s):
+                        bids_name_dict[modality_type]['modality_label'] = modality_label
+                        bids_name_dict[modality_type]['task'] = task
+                        bids_name_dict[modality_type][k1] = vb
+                    else:
+                        bids_name_dict[modality_type]['modality_label'] = modality_label
+                        bids_name_dict[modality_type]['task'] = task
     return bids_name_dict
diff --git a/convert_source/cs_utils/utils.py b/convert_source/cs_utils/utils.py
@@ -376,9 +376,9 @@ def gzip_file(file: str,
     # Check if native method was enabled.
     if native:
         if platform.system().lower() == 'windows':
-            native = False
+            native: bool = False
         else:
-            native = True
+            native: bool = True
 
     # Check if the file exists
     if os.path.exists(file):
@@ -450,9 +450,9 @@ def gunzip_file(file: str,
     # Check if native method was enabled.
     if native:
         if platform.system().lower() == 'windows':
-            native = False
+            native: bool = False
         else:
-            native = True
+            native: bool = True
 
     # Check if the file exists
     if os.path.exists(file):
@@ -963,18 +963,21 @@ def glob_dcm(dcm_dir: str) -> List[str]:
 
     for dir_ in dcm_dir_list:
         for root, dirs, files in os.walk(dir_):
-            # Only need the first DICOM file
-            tmp_dcm_file = files[0]
-            tmp_dcm_dir = root
-            tmp_file = os.path.join(tmp_dcm_dir, tmp_dcm_file)
-
-            # Old implementation - need to test with current use cases
-            dcm_files.append(tmp_file)
-            break
-
-            # if '.dcm' in tmp_file:
-            #     dcm_files.append(tmp_file)
-            #     break
+            try:
+                # Only need the first DICOM file
+                tmp_dcm_file = files[0]
+                tmp_dcm_dir = root
+                tmp_file = os.path.join(tmp_dcm_dir, tmp_dcm_file)
+
+                # Old implementation - need to test with current use cases
+                dcm_files.append(tmp_file)
+                break
+
+                # if '.dcm' in tmp_file:
+                #     dcm_files.append(tmp_file)
+                #     break
+            except IndexError:
+                continue
     return dcm_files
 
 def glob_img(img_dir: str) -> List[str]:
@@ -1317,7 +1320,6 @@ def comp_dict(d1: Dict,
         
     Raises:
         KeyError: Error that arises if input dictionaries do not have matching keys.
-        ValueError: Error that arises if one or more of the keys in either dictionary map NoneType values.
     """
     for k in d1:
         if (k not in d2):
@@ -1340,7 +1342,6 @@ def comp_dict(d1: Dict,
                         print (path, ":")
                         print (" - ", k," : ", d1[k])
                         print (" + ", k," : ", d2[k])
-                    raise ValueError("One or both input BIDS dictionaries map to NoneType values.")
     return True
 
 def depth(d: Dict) -> int:
@@ -1692,4 +1693,55 @@ def _is_gzipped(file: str) -> bool:
             #   'utf-8' codec cannot decode byte 0x8b in position 1.
             return f.read(2).encode("utf-8").hex() == GZIP_MAGIC_NUMBER
         except UnicodeDecodeError:
-            return True
+            return True
+
+def sym_link(src: str,
+             tar: str,
+             native: Optional[bool] = False
+            ) -> None:
+    """Performs symbolic linking of some input source file or directory
+    to some target output file. The symbolic linking can be performed using 
+    the UNIX system's native linking tools or via python's linking tools.
+
+    NOTE:
+        * ``Windows`` platforms require running this funciton with elevated privileges as this operation cannot be performed otherwise. 
+
+    Usage example:
+        >>> sym_link(src='<source_file/directory>',
+                     tar='<target_file>',
+                     native=True)
+        ...
+
+    Arguments:
+        src: Input source file or directory.
+        tar: Output target file that is linked to the source file or directory.
+        native: Use native UNIX linking tool instead of python's symbolic linking tool.
+
+    Returns:
+        None
+    
+    Raises:
+        FileNotFoundError: Error that arises should the source directory/file not exist.
+    """
+    # Check if native method was enabled.
+    if native:
+        if platform.system().lower() == 'windows':
+            native: bool = False
+        else:
+            native: bool = True
+
+    # Check if source file or directory exists
+    if os.path.exists(src):
+        pass
+    else:
+        raise FileNotFoundError("Cannot symbollicaly link a file or directory that does not exist.")
+
+    # Perform native of pythonic symbolic linking
+    if native:
+        link_cmd: Command = Command("ln")
+        link_cmd.cmd_list.append("-s")
+        link_cmd.cmd_list.append(src)
+        link_cmd.cmd_list.append(tar)
+        link_cmd.run()
+    else:
+        os.symlink(src,tar)
diff --git a/convert_source/tests/03_utils_test.py b/convert_source/tests/03_utils_test.py
@@ -238,8 +238,13 @@ def test_comp_dict_funcs():
     assert comp_dict(d1,d2) == True
     with pytest.raises(KeyError):
         assert comp_dict(d1,d3) == False
-    with pytest.raises(ValueError):
-        assert comp_dict(d3,d4)
+    # This assertion is no longer valid
+    #   as a result of allowing NoneType
+    #   values to be mapped in either
+    #   dictionary.
+    # 
+    # with pytest.raises(ValueError):
+    #     assert comp_dict(d3,d4)
     assert depth(d1) == 3
     assert depth(d2) == 3
     assert depth(d3) == 3

diff --git a/convert_source/tests/helper.scripts/test.2.config.yml b/convert_source/tests/helper.scripts/test.2.config.yml
@@ -25,7 +25,6 @@ modality_search:
             rest: 
                 - rsfMR
                 - rest
-                - FFE
                 - FEEPI
         # ASL (arterial spin labeling) contrast
         cbv:
@@ -76,11 +75,6 @@ bids_search:
                 ce:
                 dir:
                 rec:
-            visualstrobe:
-                acq:
-                ce:
-                dir:
-                rec:
         # ASL (arterial spin labeling) contrast
         cbv:
             rest:
@@ -133,11 +127,6 @@ bids_map:
                 ce:
                 dir:
                 rec:
-            visualstrobe:
-                acq:
-                ce:
-                dir:
-                rec:
         # ASL (arterial spin labeling) contrast
         cbv:
             rest:

diff --git a/convert_source/tests/helper.scripts/test.file_structure.sh b/convert_source/tests/helper.scripts/test.file_structure.sh
@@ -9,7 +9,7 @@
 
 #######################################
 # Usage function. Prints help and then
-# exits.
+#   exits.
 # Globals:
 #   None
 # Arguments:

diff --git a/convert_source/version.txt b/convert_source/version.txt
@@ -1 +1 @@
-0.2.0a7
+0.2.0a8