Merge pull request #41 from AdebayoBraimah/dev5

Dev5

.circleci/config.yml

@@ -12,14 +12,14 @@ jobs:
     steps:
       - checkout
       - run:
-          command: python -m pip install pytest pytest-html -r requirements.txt --user
+          command: python -m pip install pytest pytest-html pytest-cov -r requirements.txt --user
           name: Install-deps
       - run:
           command: chmod -R 755 convert_source/tests
           name: Change file permissions
       - run:
           command: |
-            pytest --junitxml=test-reports/junit.xml --html=test-reports/pytest_report.html --self-contained-html convert_source/tests
+            pytest --junitxml=test-reports/junit.xml --html=test-reports/pytest_report.html --self-contained-html --cov=convert_source convert_source/tests
           name: Run unit tests
       - store_test_results:
           path: test-reports

CHANGES.rst

@@ -1,6 +1,16 @@
 CHANGES
 =========
 
+0.2.0a9
+---------
+
+This version is an alpha release that contains several bug fixes and updates.
+
+* BUG FIX: Fixed issue in which multiple converted NIFTI files would throw index error exception during BIDS renaming.
+* BUG FIX: Added minimal type checking for several BIDS metadata fields
+* BUG FIX: Fixed bug in which if par/nii was in the filepath, the source image file could be misclassified - thus subsequently throwing errors.
+* UPDATE: Added option to throw exceptions for PAR multi-echo data. At the moment, without test data correctly handling cases of multi-echo data are not possible for PAR REC data.
+
 0.2.0a8
 ---------
 

convert_source/batch_convert.py

@@ -727,22 +727,25 @@ def _get_bids_name_args(bids_name_dict: Dict,
     return tuple(params_var)
 
 def make_bids_name(bids_name_dict: Dict,
-                    modality_type: str
-                   ) -> Tuple[str,str,str,str]:
+                    modality_type: str,
+                    num_imgs: Optional[int] = 4
+                   ) -> List[str]:
     """Creates a BIDS compliant filename given a BIDS name description dictionary, and the modality type.
 
     Usage example:
         >>> make_bids_name(bids_name_dict=bids_dict,
-        ...                 modality_type="anat")
+        ...                modality_type="anat",
+        ...                num_imgs=1)
         ...
         "sub-001_ses-001_run-01_T1w"
         
     Arguments:
         bids_name_dict: BIDS name description dictionary.
         modality_type: Modality type.
+        num_imgs: Number of medical images to be re-named.
 
     Returns:
-        BIDS compliant filename string.
+        List of BIDS compliant filenames.
     """
 
     bids_keys: List[str] = list(bids_name_dict[modality_type].keys())
@@ -785,75 +788,56 @@ def make_bids_name(bids_name_dict: Dict,
     if rec and ('rec' in bids_keys):
         f_name += f"_rec-{rec}"
 
-    # Set multiple run names
-    run1: str = str(run)
-    run2: str = add_to_zeropadded(run,1)
-    run3: str = add_to_zeropadded(run,2)
-    run4: str = add_to_zeropadded(run,3)
-
-    f_name1: str = f_name + f"_run-{run1}"
-    f_name2: str = f_name + f"_run-{run2}"
-    f_name3: str = f_name + f"_run-{run3}"
-    f_name4: str = f_name + f"_run-{run4}"
-
-    if echo and ('echo' in bids_keys):
-        f_name1 += f"_echo-{echo}"
-        f_name2 += f"_echo-{echo}"
-        f_name3 += f"_echo-{echo}"
-        f_name4 += f"_echo-{echo}"
+    # Set name list in the case of 
+    #   multiple images
+    name_list: List[str] = []
+
+    for run_num in range(0,num_imgs):
+        run_id: str = add_to_zeropadded(run,run_num)
+        f_name_tmp: str = f_name + f"_run-{run_id}"
+
+        if echo and ('echo' in bids_keys):
+            f_name_tmp += f_name_tmp + f"_echo-{echo}"
+
+        name_list.append(f_name_tmp)
 
     if modality_type.lower() == 'fmap':
         if case1 and mag2:
-            f_name1: str = f_name1 + "_phasediff"
-            f_name2: str = f_name1 + "_magnitude1"
-            f_name3: str = f_name1 + "_magnitude2"
-            return (f_name1,
-                   f_name2,
-                   f_name3,
-                   "")
+            f_name1: str = name_list[0] + "_phasediff"
+            f_name2: str = name_list[0] + "_magnitude1"
+            f_name3: str = name_list[0] + "_magnitude2"
+            return ([f_name1,
+                     f_name2,
+                     f_name3])
         elif case1:
-            f_name1: str = f_name1 + "_phasediff"
-            f_name2: str = f_name1 + "_magnitude1"
-            return (f_name1,
-                   f_name2,
-                   "",
-                   "")
+            f_name1: str = name_list[0] + "_phasediff"
+            f_name2: str = name_list[0] + "_magnitude1"
+            return ([f_name1,
+                     f_name2])
         elif case2:
-            f_name1: str = f_name1 + "_phase1"
-            f_name2: str = f_name1 + "_phase2"
-            f_name3: str = f_name1 + "_magnitude1"
-            f_name4: str = f_name1 + "_magnitude2"
-            return (f_name1,
-                   f_name2,
-                   f_name3,
-                   f_name4)
+            f_name1: str = name_list[0] + "_phase1"
+            f_name2: str = name_list[0] + "_phase2"
+            f_name3: str = name_list[0] + "_magnitude1"
+            f_name4: str = name_list[0] + "_magnitude2"
+            return ([f_name1,
+                     f_name2,
+                     f_name3,
+                     f_name4])
         elif case3:
-            f_name1: str = f_name1 + "_magnitude"
-            f_name2: str = f_name1 + "_fieldmap"
-            return (f_name1,
-                   f_name2,
-                   "",
-                   "")
+            f_name1: str = name_list[0] + "_magnitude"
+            f_name2: str = name_list[0] + "_fieldmap"
+            return ([f_name1,
+                     f_name2])
         elif case4:
             modality_label = bids_name_dict[modality_type]['modality_label']
-            f_name1 += f"_{modality_label}"
-            f_name2 += f"_{modality_label}"
-            f_name3 += f"_{modality_label}"
-            f_name4 += f"_{modality_label}"
-            return (f_name1,
-                    f_name2,
-                    f_name3,
-                    f_name4)
+            for i in range(0,len(name_list)):
+                name_list[i] += f"_{modality_label}"
+            return name_list
     else:
         modality_label = bids_name_dict[modality_type]['modality_label']
-        f_name1 += f"_{modality_label}"
-        f_name2 += f"_{modality_label}"
-        f_name3 += f"_{modality_label}"
-        f_name4 += f"_{modality_label}"
-        return (f_name1,
-                f_name2,
-                f_name3,
-                f_name4)
+        for i in range(0,len(name_list)):
+                name_list[i] += f"_{modality_label}"
+        return name_list
 
 def source_to_bids(sub_data: SubDataInfo,
                    bids_name_dict: Dict,
@@ -1043,7 +1027,7 @@ def source_to_bids(sub_data: SubDataInfo,
                                                            out_dir=out_data_dir)
 
                 # Ensure that DWI and Fieldmap data are not kept as unknown
-                # by calling nifti_to_bids if that is the case.
+                #   by calling nifti_to_bids if that is the case.
                 if img_data.bvals[0] and img_data.bvecs[0] and not modality_type:
                     modality_type = 'dwi'
                     modality_label = 'dwi'
@@ -1103,11 +1087,10 @@ def source_to_bids(sub_data: SubDataInfo,
                     pass
                 else:
                     modality_type: str = "unknown"
-
-                [bids_1, bids_2, bids_3, bids_4] = make_bids_name(bids_name_dict=bids_name_dict,
-                                                                   modality_type=modality_type)
 
-                bids_names: List[str] = [bids_1, bids_2, bids_3, bids_4]
+                bids_names: List[str] = make_bids_name(bids_name_dict=bids_name_dict,
+                                                       modality_type=modality_type,
+                                                       num_imgs=len(img_data.imgs))
 
                 # Image data return lists
                 imgs: List[str] = []
@@ -1394,11 +1377,10 @@ def nifti_to_bids(sub_data: SubDataInfo,
                 pass
             else:
                 modality_type: str = "unknown"
-
-            [bids_1, bids_2, bids_3, bids_4] = make_bids_name(bids_name_dict=bids_name_dict,
-                                                            modality_type=modality_type)
-
-            bids_names: List[str] = [bids_1, bids_2, bids_3, bids_4]
+
+            bids_names: List[str] = make_bids_name(bids_name_dict=bids_name_dict,
+                                                   modality_type=modality_type,
+                                                   num_imgs=len(img_data.imgs))
 
             # Image data return lists
             imgs: List[str] = []

convert_source/cs_utils/bids_info.py

@@ -116,6 +116,9 @@ def construct_bids_dict(meta_dict: Optional[Dict] = None,
 
     # Update BIDS ordered array
     meta_list: List[str] = list(meta_dict.keys())
+    json_list: List[str] = list(json_dict.keys())
+
+    ordered_array.extend(json_list)
     ordered_array.extend(meta_list)
     ordered_list: List[str] = []
 

convert_source/cs_utils/utils.py

@@ -11,12 +11,16 @@
 import pydicom
 import numpy as np
 
-from collections import deque
 from json import JSONDecodeError
 from copy import deepcopy
 from shutil import copy
 from tqdm import tqdm
 
+from collections import (
+    deque,
+    OrderedDict
+)
+
 from typing import (
     List, 
     Dict, 
@@ -572,7 +576,6 @@ def update_json(json_file: str,
     Returns: 
         Updated JSON file.
     """
-
     # Check if JSON file exists, if not, then create JSON file
     if not os.path.exists(json_file):
         with open(json_file,"w"): pass
@@ -618,11 +621,12 @@ def dict_multi_update(dictionary: Optional[Dict] = None,
     if dictionary:
         new_dict: Dict = deepcopy(dictionary)
     else:
-        new_dict: Dict = {}
+        new_dict: OrderedDict = OrderedDict({})
 
     for key,item in kwargs.items():
         tmp_dict: Dict = {key:item}
-        new_dict.update(tmp_dict)
+        if (isinstance(item,int))or (isinstance(item,float)) or (isinstance(item,str)) or (isinstance(item,list)):
+            new_dict.update(tmp_dict)
     return new_dict
 
 def get_bvals(bval_file: Optional[str] = ""
@@ -1511,7 +1515,10 @@ def get_dcm_scan_tech(dcm_file: str,
     ds = pydicom.dcmread(dcm_file)
 
     # Search DICOM header for Scan Technique
-    dcm_scan_tech_str = str(ds[0x2001,0x1020])
+    try:
+        dcm_scan_tech_str: str = str(ds[0x2001,0x1020])
+    except KeyError:
+        dcm_scan_tech_str: str = ""
 
     # Use dictionary to search in string
     for i in search_arr:
@@ -1553,7 +1560,7 @@ def get_dcm_scan_tech(dcm_file: str,
     dcm_fields: List[str] = ['SeriesDescription', 'ImageType', 'ProtocolName']
 
     for dcm_field in dcm_fields:
-            dcm_scan_tech_str = str(eval(f"ds.{dcm_field}")) # This makes me dangerously uncomfortable
+            dcm_scan_tech_str: str = str(eval(f"ds.{dcm_field}")) # This makes me dangerously uncomfortable
 
             # Use dictionary to search in string
             for i in search_arr:

convert_source/imgio/niio.py

@@ -112,7 +112,7 @@ def get_data_params(file: str,
                          "TotalReadoutTime": tot_read_time,
                          "AcquisitionDuration": scan_time,
                          "SourceDataFormat": source_format})
-    elif 'par' in file.lower():
+    elif '.par' in file.lower():
         wfs: float = get_wfs(file)
         red_fact: float = par_red_fact(file)
         mb: int = par_mb(file)
@@ -133,7 +133,7 @@ def get_data_params(file: str,
                          "EchoTime": echo_time,
                          "FlipAngle": flip_angle,
                          "SourceDataFormat": source_format})
-    elif 'nii' in file.lower():
+    elif '.nii' in file.lower():
         tr: Union[float,str] = get_nii_tr(file)
         source_format: str = "NIFTI"
         tmp_dict.update({"RepetitionTime": tr,

convert_source/imgio/pario.py

@@ -150,7 +150,8 @@ def get_scan_time(par_file: str) -> Union[float,str]:
     return scan_time
 
 def get_echo_time(par_file: str,
-                 tmp_dir: Optional[str] = None
+                 tmp_dir: Optional[str] = None,
+                 raise_exc: Optional[bool] = False
                  ) -> float:
     """Reads the echo time (TE, in sec.) from a PAR header file.
 
@@ -167,9 +168,14 @@ def get_echo_time(par_file: str,
     Arguments:
         par_file: PAR header file.
         tmp_dir: Path to temporary directory.
+        raise_exc: Raise exception in the case of multi-echo acquisitions.
         
     Returns:
-        Echo time as a float.
+        Echo time as a float or ``None`` in the case of multi-echo data.
+    
+    Raises:
+        PARfileReadError: Exception that is raised if multi-echo PAR files 
+            are used as inputs.
     """
     if tmp_dir:
         pass
@@ -189,12 +195,16 @@ def get_echo_time(par_file: str,
         _ = tmp.rm_tmp_dir(rm_parent=False)
 
     if len(list(np.unique(mat[0:,16]))) > 1:
-        raise PARfileReadError(f"Two or more unique echo times were found in {par_file}. Please check.")
+        if raise_exc:
+            raise PARfileReadError(f"Two or more unique echo times were found in {par_file}. Please check.")
+        else:
+            return None
     else:
         return float(round(Decimal(float(np.unique(mat[0:,16]))/1000),4))
 
 def get_flip_angle(par_file: str,
-                   tmp_dir: Optional[str] = None
+                   tmp_dir: Optional[str] = None,
+                   raise_exc: Optional[bool] = False
                   ) -> float:
     """Reads the flip angle (in degrees) from a PAR header file.
 
@@ -211,9 +221,13 @@ def get_flip_angle(par_file: str,
     Arguments:
         par_file: PAR header file.
         tmp_dir: Path to temporary directory.
+        raise_exc: Raise exception in the case of multiple flip angles are found.
         
     Returns:
-        Flip angle as a float.
+        Flip angle as a float or None if multiple flip angles are found.
+    
+    Raises:
+        PARfileReadError: Exception that is raised if input PAR file contains multiple flip angles.
     """
     if tmp_dir:
         pass
@@ -233,6 +247,9 @@ def get_flip_angle(par_file: str,
         _ = tmp.rm_tmp_dir(rm_parent=False)
 
     if len(list(np.unique(mat[0:,21]))) > 1:
-        raise PARfileReadError(f"Two or more unique flip angles were found in {par_file}. Please check.")
+        if raise_exc:
+            raise PARfileReadError(f"Two or more unique flip angles were found in {par_file}. Please check.")
+        else:
+            return None
     else:
         return float(np.unique(mat[0:,21]))

convert_source/version.txt

@@ -1 +1 @@
-0.2.0a8
+0.2.0a9