diff --git a/_modules/trx/fetcher.html b/_modules/trx/fetcher.html index eed9150..9dceb83 100644 --- a/_modules/trx/fetcher.html +++ b/_modules/trx/fetcher.html @@ -352,7 +352,7 @@

Source code for trx.fetcher

     if 'TRX_HOME' in os.environ:
         trx_home = os.environ['TRX_HOME']
     else:
-        trx_home = os.path.join(os.path.expanduser('~'), '.tee_ar_ex/')
+        trx_home = os.path.join(os.path.expanduser('~'), '.tee_ar_ex')
     return trx_home
diff --git a/_modules/trx/io.html b/_modules/trx/io.html index 5883000..f016206 100644 --- a/_modules/trx/io.html +++ b/_modules/trx/io.html @@ -444,7 +444,8 @@

Source code for trx.io

     else:
         if not isinstance(tractogram_obj, tmm.TrxFile):
             tractogram_obj = tmm.TrxFile.from_sft(tractogram_obj)
-        tmm.save(tractogram_obj, tractogram_filename)
+ tmm.save(tractogram_obj, tractogram_filename) + tractogram_obj.close() diff --git a/_modules/trx/trx_file_memmap.html b/_modules/trx/trx_file_memmap.html index 0970e32..81309a9 100644 --- a/_modules/trx/trx_file_memmap.html +++ b/_modules/trx/trx_file_memmap.html @@ -615,7 +615,6 @@

Source code for trx.trx_file_memmap

                     "An undeclared group ({}) has " "data_per_group.".format(
                         dpg)
                 )
-
     return trx
@@ -710,7 +709,6 @@

Source code for trx.trx_file_memmap

 
             dtype_size = np.dtype(ext[1:]).itemsize
             size = os.path.getsize(elem_filename) / dtype_size
-
             if size.is_integer():
                 files_pointer_size[elem_filename] = 0, int(size)
             elif os.path.getsize(elem_filename) == 1:
@@ -923,7 +921,6 @@ 
Source code for trx.trx_file_memmap
 
     copy_trx = trx.deepcopy()
     copy_trx.resize()
-
     tmp_dir_name = copy_trx._uncompressed_folder_handle.name
     if ext in [".zip", ".trx"]:
         zip_from_folder(tmp_dir_name, filename, compression_standard)
@@ -950,11 +947,11 @@ 
Source code for trx.trx_file_memmap
 
     """
     with zipfile.ZipFile(filename, mode="w", compression=compression_standard) as zf:
-        for root, dirs, files in os.walk(directory):
+        for root, _, files in os.walk(directory):
             for name in files:
-                tmp_filename = os.path.join(root, name)
-                zf.write(tmp_filename, tmp_filename.replace(
-                    directory + "/", ""))

+                curr_filename = os.path.join(root, name)
+                tmp_filename = curr_filename.replace(directory, "")[1:]
+                zf.write(curr_filename, tmp_filename)

 
 
 
@@ -1490,9 +1487,11 @@ 
Source code for trx.trx_file_memmap
                 # This is for Unix
                 if os.name != 'nt' and folder.startswith(root.rstrip("/")):
                     folder = folder.replace(root, "").lstrip("/")
-                # These two are for Windows
-                elif os.path.isdir(folder) and os.path.basename(folder) in ['dpg', 'dpv', 'dps']:
+                # These three are for Windows
+                elif os.path.isdir(folder) and os.path.basename(folder) in ['dpv', 'dps', 'groups']:
                     folder = os.path.basename(folder)
+                elif os.path.basename(os.path.dirname(folder)) == 'dpg':
+                    folder = os.path.join('dpg', os.path.basename(folder))
                 else:
                     folder = ''
 
@@ -2030,6 +2029,7 @@ 
Source code for trx.trx_file_memmap
         save(trx, tmp_dir.name)
         trx.close()
         trx = load_from_directory(tmp_dir.name)
+        trx._uncompressed_folder_handle = tmp_dir
 
         sft.to_space(old_space)
         sft.to_origin(old_origin)
diff --git a/_modules/trx/workflows.html b/_modules/trx/workflows.html
index dc2adb5..658287b 100644
--- a/_modules/trx/workflows.html
+++ b/_modules/trx/workflows.html
@@ -389,7 +389,7 @@ 
Source code for trx.workflows
                 f_out.writelines(f_in)
                 sft = load_tractogram('tmp.trk', 'same',
                                       bbox_valid_check=False)
-                os.remove('tmp.trk')
+            os.remove('tmp.trk')
     elif in_ext == '.trk':
         sft = load_tractogram(in_dsi_tractogram, 'same',
                               bbox_valid_check=False)
@@ -603,7 +603,7 @@ 
Source code for trx.workflows
 
     if not isinstance(tractogram_obj, StatefulTractogram):
         sft = tractogram_obj.to_sft()
-        tractogram_obj.close()
+        # tractogram_obj.close()
     else:
         sft = tractogram_obj
 
@@ -761,7 +761,6 @@ 
Source code for trx.workflows
                 curr_filename = os.path.join(tmp_dir_name, 'dps', '{}.{}{}'.format(
                     os.path.basename(os.path.splitext(arg[0])[0]), dim, arg[1]))
                 curr_arr.tofile(curr_filename)
-
         if groups:
             os.mkdir(os.path.join(tmp_dir_name, 'groups'))
             for arg in groups: