Merge pull request #115 from dvm-shlee/main

0.3.8, hotfix

brkraw/__init__.py

@@ -1,6 +1,6 @@
 from .lib import *
 
-__version__ = '0.3.8'
+__version__ = '0.3.10'
 __all__ = ['BrukerLoader', '__version__']
 
 

brkraw/lib/backup.py

@@ -137,7 +137,7 @@ def set_arc(self, arc_fname, arc_dir, raw_dir):
                 garbage = True
                 crashed = True
 
-            if raw_dname is not None:
+            if raw_dname != None:
                 r = self.get_rpath_obj(raw_dname)
             else:
                 r = None
@@ -265,7 +265,7 @@ def _parse_info(self):
         # update raw dataset information (raw dataset cache will remain even its removed)
         print('\nScanning raw dataset cache...')
         for r in tqdm.tqdm(self.raw_data[:], bar_format=_bar_fmt):
-            if r.path is not None:
+            if r.path != None:
                 if not os.path.exists(os.path.join(self._rpath, r.path)):
                     if not r.removed:
                         r.removed = True
@@ -300,7 +300,7 @@ def _parse_info(self):
 
     def is_same_as_raw(self, filename):
         arc = BrukerLoader(os.path.join(self._apath, filename))
-        if arc.pvobj.path is not None:
+        if arc.pvobj.path != None:
             raw_path = os.path.join(self._rpath, arc.pvobj.path)
             if os.path.exists(raw_path):
                 raw = BrukerLoader(raw_path)
@@ -495,7 +495,7 @@ def clean(self):
                     print('\nStart removing {} archived data...'.format(label.upper()))
                     if len(dset.items()):
                         for raw_dname, arcs in dset.items():
-                            if raw_dname is not None:
+                            if raw_dname != None:
                                 raw_path = os.path.join(self._rpath, raw_dname)
                                 if os.path.exists(raw_path):
                                     r_size, r_unit = get_dirsize(raw_path)

brkraw/lib/errors.py

@@ -22,13 +22,13 @@ def __init__(self, file_name=None, data_type=None):
         self.file_name = None
         self.data_type = None
 
-        if file_name is not None:
+        if file_name != None:
             self.file_name = os.path.basename(file_name)
             if os.path.isdir(file_name):
                 object_type = 'directory'
             else:
                 object_type = 'file'
-            if data_type is not None:
+            if data_type != None:
                 self.data_type = data_type
                 self.message = "The {} '{}' is not valid {}".format(object_type,
                                                                     self.file_name,
@@ -45,7 +45,7 @@ class ArchiveFailedError(Error):
     file_name = None
 
     def __init__(self, file_name=None):
-        if file_name is not None:
+        if file_name != None:
             self.file_name = os.path.basename(file_name)
             self.message = "The data '{}' is not archived".format(
                 self.file_name)
@@ -58,7 +58,7 @@ class RemoveFailedError(Error):
     file_name = None
 
     def __init__(self, file_name=None):
-        if file_name is not None:
+        if file_name != None:
             self.file_name = os.path.basename(file_name)
             self.message = "The file '{}' is not removed".format(
                 self.file_name)
@@ -72,11 +72,11 @@ class RenameFailedError(Error):
     file2_name = None
 
     def __init__(self, file1_name=None, file2_name=None):
-        if file1_name is not None:
+        if file1_name != None:
             self.file1_name = os.path.basename(file1_name)
-        if file2_name is not None:
+        if file2_name != None:
             self.file2_name = os.path.basename(file2_name)
-        if (self.file1_name is not None) and (self.file2_name is not None):
+        if (self.file1_name != None) and (self.file2_name != None):
             self.message = "Rename failed to execute from:'{}' to:'{}'".format(self.file1_name,
                                                                                self.file2_name)
         else:

brkraw/lib/loader.py

@@ -255,7 +255,7 @@ def swap_slice_axis(group_id_, dataobj_):
                 dataobj_ = np.swapaxes(dataobj_, 2, slice_axis_)
             return dataobj_
 
-        if fg_info['frame_type'] is not None:
+        if fg_info['frame_type'] != None:
             if group_id[0] == 'FG_SLICE':
                 pass
 
@@ -327,9 +327,9 @@ def get_niftiobj(self, scan_id, reco_id, crop=None, slope=False, offset=False):
         affine = self._get_affine(visu_pars, method)
 
         data_slp, data_off = self._get_dataslp(visu_pars)
-        if isinstance(data_slp, list) and slope is not None:
+        if isinstance(data_slp, list) and slope != None:
             slope = True
-            if isinstance(data_off, list) and offset is not None:
+            if isinstance(data_off, list) and offset != None:
                 offset = True
 
         imgobj = self.get_dataobj(scan_id, reco_id, slope=slope, offset=offset)
@@ -359,7 +359,7 @@ def get_niftiobj(self, scan_id, reco_id, crop=None, slope=False, offset=False):
                     f = multiply_all(imgobj_.shape[3:])
                     # all converted nifti must be 4D
                     imgobj_ = imgobj_.reshape([x, y, z, f])
-                if crop is not None:
+                if crop != None:
                     if crop[0] is None:
                         niiobj_ = Nifti1Image(imgobj_[..., :crop[1]], affine)
                     elif crop[1] is None:
@@ -377,7 +377,7 @@ def get_niftiobj(self, scan_id, reco_id, crop=None, slope=False, offset=False):
                 f = multiply_all(imgobj.shape[3:])
                 # all converted nifti must be 4D
                 imgobj = imgobj.reshape([x, y, z, f])
-        if crop is not None:
+        if crop != None:
             if crop[0] is None:
                 niiobj = Nifti1Image(imgobj[..., :crop[1]], affine)
             elif crop[1] is None:
@@ -511,7 +511,7 @@ def _parse_json(self, scan_id, reco_id, metadata=None):
             val = meta_get_value(v, acqp, method, visu_pars)
             if k in ['PhaseEncodingDirection', 'SliceEncodingDirection']:
                 # Convert the encoding direction meta data into BIDS format
-                if val is not None:
+                if val != None:
                     if isinstance(val, int):
                         val = encdir_dic[val]
                     else:
@@ -551,7 +551,7 @@ def _parse_json(self, scan_id, reco_id, metadata=None):
 
     def save_json(self, scan_id, reco_id, filename, dir='./', metadata=None, condition=None):
         json_obj = self._parse_json(scan_id, reco_id, metadata)
-        if condition is not None:
+        if condition != None:
             code, idx = condition
             if code == 'me':    # multi-echo
                 if 'EchoTime' in json_obj.keys():
@@ -599,7 +599,7 @@ def get_scan_time(self, visu_pars=None):
             # date
             date = dt.datetime.strptime(re.sub(pattern_1, r'\2', subject_date), '%d %b %Y').date()
             # end time
-            if visu_pars is not None:
+            if visu_pars != None:
                 last_scan_time = get_value(visu_pars, 'VisuAcqDate')
                 last_scan_time = dt.time(*map(int, re.sub(pattern_1, r'\1', last_scan_time).split(':')))
                 acq_time = get_value(visu_pars, 'VisuAcqScanTime') / 1000.0
@@ -616,7 +616,7 @@ def get_scan_time(self, visu_pars=None):
             date = dt.date(*map(int, re.sub(pattern_2, r'\1', subject_date).split('-')))
 
             # end date
-            if visu_pars is not None:
+            if visu_pars != None:
                 scan_time = get_value(visu_pars, 'VisuCreationDate')[0]
                 scan_time = dt.time(*map(int, re.sub(pattern_2, r'\2', scan_time).split(':')))
                 return dict(date=date,
@@ -785,7 +785,7 @@ def _set_nifti_header(self, niiobj, visu_pars, method, slope, offset):
         else:
             niiobj.header.set_xyzt_units('mm')
         if not slope:
-            if slope is not None:
+            if slope != None:
                 if isinstance(data_slp, list):
                     raise InvalidApproach('Invalid slope size;'
                                           'The vector type scl_slope cannot be set in nifti header.')
@@ -795,7 +795,7 @@ def _set_nifti_header(self, niiobj, visu_pars, method, slope, offset):
         else:
             niiobj.header['scl_slope'] = 1
         if not offset:
-            if offset is not None:
+            if offset != None:
                 if isinstance(data_off, list):
                     raise InvalidApproach('Invalid offset size;'
                                           'The vector type scl_offset cannot be set in nifti header.')
@@ -814,7 +814,7 @@ def _get_temp_info(self, visu_pars):
         total_time = get_value(visu_pars, 'VisuAcqScanTime')
         fg_info = self._get_frame_group_info(visu_pars)
         parser = []
-        if fg_info['frame_type'] is not None:
+        if fg_info['frame_type'] != None:
             for id, fg in enumerate(fg_info['group_id']):
                 if not re.search('slice', fg, re.IGNORECASE):
                     parser.append(fg_info['matrix_shape'][id])
@@ -1004,7 +1004,7 @@ def get_axis_orient(orient_matrix):
         orient_matrix = get_value(visu_pars, 'VisuCoreOrientation').tolist()
         slice_info = self._get_slice_info(visu_pars)
         slice_position = get_value(visu_pars, 'VisuCorePosition')
-        if self._override_position is not None: # add option to override
+        if self._override_position != None: # add option to override
             subj_position = self._override_position
         else:
             subj_position = get_value(visu_pars, 'VisuSubjectPosition')
@@ -1062,7 +1062,7 @@ def get_axis_orient(orient_matrix):
             oorder_parser = get_axis_orient(omatrix_parser)
             vposition_parser = slice_position
 
-        if self._override_type is not None: # add option to override
+        if self._override_type != None: # add option to override
             subj_type = self._override_type
         else:
             subj_type = get_value(visu_pars, 'VisuSubjectType')    
@@ -1147,7 +1147,7 @@ def _get_matrix_size(self, visu_pars, dataobj=None):
                 if num_temporal_frame > 1:
                     matrix_size.append(num_temporal_frame)
 
-        if dataobj is not None:
+        if isinstance(dataobj, np.ndarray):
             # matrix size inspection
             dataobj_shape = dataobj.shape[0]
             if multiply_all(matrix_size) != dataobj_shape:

brkraw/lib/orient.py

@@ -146,7 +146,7 @@ def get_origin(slice_position, gradient_orient):
     max_delta_axis = np.argmax([dx, dy, dz])
     rx, ry, rz = [None, None, None]
 
-    if gradient_orient is not None:
+    if isinstance(gradient_orient, np.ndarray):
         zmat = np.zeros(gradient_orient[0].shape)
         for cid, col in enumerate(gradient_orient[0].T):
             yid = np.argmax(abs(col))

brkraw/lib/pvobj.py

@@ -33,7 +33,7 @@ def _reset(self):
         self._2dseq = dict()
 
     def _update_studyinfo(self):
-        if self._subject is not None:
+        if self._subject != None:
             subject = self._subject
             self.user_account   = subject.headers['OWNER']
             self.subj_id        = get_value(subject, 'SUBJECT_id')

brkraw/lib/utils.py

@@ -1,4 +1,4 @@
-from .errors import UnexpectedError
+from .errors import *
 from .reference import *
 import re
 import os
@@ -30,7 +30,7 @@ def load_param(stringlist):
     for line_num, line in enumerate(stringlist):
         regex_obj = re.match(ptrn_param, line)
         # if line is key=value pair
-        if regex_obj is not None:
+        if regex_obj != None:
             # parse key and value
             key = re.sub(ptrn_param, r'\g<key>', line)
             value = re.sub(ptrn_param, r'\g<value>', line)
@@ -105,7 +105,7 @@ def convert_data_to(data, shape):
                         cont_parser = []
                         for cont in map(str.strip, parsed.group('contents').split(',')):
                             cont = convert_data_to(cont, -1)
-                            if cont is not None:
+                            if cont != None:
                                 cont_parser.append(cont)
                         if key not in parser.keys():
                             parser[key] = []
@@ -120,7 +120,7 @@ def convert_data_to(data, shape):
                 else:
                     is_array = re.findall(ptrn_array, data)
                     # parse data shape
-                    if shape is not -1:
+                    if shape != -1:
                         shape = re.sub(ptrn_array, r'\g<array>', shape)
                         if ',' in shape:
                             shape = [convert_string_to(c) for c in shape.split(',')]
@@ -191,7 +191,7 @@ def meta_get_value(value, acqp, method, visu_pars):
         max_index = len(value) - 1
         for i, vi in enumerate(value):
             val = meta_get_value(vi, acqp, method, visu_pars)
-            if val is not None:
+            if val != None:
                 if val == vi:
                     if i == max_index:
                         parser.append(val)
@@ -228,7 +228,7 @@ def is_express(value):
 
 def meta_check_where(value, acqp, method, visu_pars):
     val = meta_get_value(value['key'], acqp, method, visu_pars)
-    if val is not None:
+    if val != None:
         if isinstance(value['where'], str):
             if value['where'] not in val:
                 return None
@@ -243,12 +243,12 @@ def meta_check_where(value, acqp, method, visu_pars):
 
 def meta_check_index(value, acqp, method, visu_pars):
     val = meta_get_value(value['key'], acqp, method, visu_pars)
-    if val is not None:
+    if val != None:
         if isinstance(value['idx'], int):
             return val[value['idx']]
         else:
             idx = meta_get_value(value['idx'], acqp, method, visu_pars)
-        if idx is not None:
+        if idx != None:
             return val[idx]
         else:
             return None
@@ -335,7 +335,6 @@ def get_filesize(file_path):
 
 def bids_validation(df, idx, key, val, num_char_allowed, dtype=None):
     import string
-    from shleeh.errors import InvalidValueInField
     col = string.ascii_uppercase[df.columns.tolist().index(key)]
     special_char = re.compile(r'[^0-9a-zA-Z]')
     str_val = str(val)
@@ -344,13 +343,13 @@ def bids_validation(df, idx, key, val, num_char_allowed, dtype=None):
         message = "{} You can't use more than {} characters.".format(loc, num_char_allowed)
         raise InvalidValueInField(message)
     matched = special_char.search(str_val)
-    if matched is not None:
+    if matched != None:
         if ' ' in matched.group():
             message = "{} Empty string is not allowed.".format(loc)
         else:
             message = "{} Special characters are not allowed.".format(loc)
         raise InvalidValueInField(message)
-    if dtype is not None:
+    if dtype != None:
         try:
             dtype(val)
         except:
@@ -361,7 +360,6 @@ def bids_validation(df, idx, key, val, num_char_allowed, dtype=None):
 
 def get_bids_ref_obj(ref_path, row):
     import json
-    from shleeh.errors import InvalidApproach
     if os.path.exists(ref_path) and ref_path.lower().endswith('.json'):
         ref_data = json.load(open(ref_path))
         ref = ref_data['common']