Export slices mask (#166)

* Export hdf5 * Exporting mask to hdf5 * Exporting all project to hdf5 * better hierachy of tags * Only exporting project * Option to export to hdf5 via command line * suffix * Added an option to not export masks * exporting to nifti * Exporting to nifti * Doing swap axes to export nii * Better extension handling * Better extension handling * fliping lr when exporting to nii

Export slices mask (#166)
* Export hdf5 * Exporting mask to hdf5 * Exporting all project to hdf5 * better hierachy of tags * Only exporting project * Option to export to hdf5 via command line * suffix * Added an option to not export masks * exporting to nifti * Exporting to nifti * Doing swap axes to export nii * Better extension handling * Better extension handling * fliping lr when exporting to nii
Thiago Franco de Moraes · GitHub
1 parent e0a64d3e
Showing 5 changed files with 143 additions and 4 deletions Show diff stats
app.py
invesalius/constants.py
invesalius/data/slice_.py
invesalius/gui/frame.py
invesalius/project.py
@@ -336,6 +336,13 @@ def parse_comand_line():
     parser.add_option("-a", "--export-to-all",
                       help="Export to STL for all mask presets.")
+    parser.add_option("--export-project",
+                      help="Export slices and mask to HDF5 or Nifti file.")
+
+    parser.add_option("--no-masks", action="store_false",
+                      dest="save_masks", default=True,
+                      help="Make InVesalius not export mask when exporting project.")
+
     options, args = parser.parse_args()
     return options, args
@@ -429,6 +436,17 @@ def check_for_export(options, suffix=&#39;&#39;, remove_surfaces=False):
         finally:
             exit(0)
+    if options.export_project:
+        from invesalius.project import Project
+        prj = Project()
+        export_filename = options.export_project
+        if suffix:
+            export_filename, ext = os.path.splitext(export_filename)
+            export_filename = u'{}-{}{}'.format(export_filename, suffix, ext)
+
+        prj.export_project(export_filename, save_masks=options.save_masks)
+        print("Saved {}".format(export_filename))
+
 def export(path_, threshold_range, remove_surface=False):
     import invesalius.constants as const
@@ -506,10 +506,11 @@ VTK_WARNING = 0
 #----------------------------------------------------------
 [ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,
-ID_PROJECT_CLOSE, ID_PROJECT_INFO, ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET,
-ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK,
-ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED, ID_MODE_NAVIGATION, ID_ANALYZE_IMPORT,
-ID_NIFTI_IMPORT, ID_PARREC_IMPORT, ID_MODE_DBS] = [wx.NewId() for number in range(19)]
+ ID_PROJECT_CLOSE, ID_EXPORT_SLICE, ID_EXPORT_MASK, ID_PROJECT_INFO,
+ ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET, ID_PRINT_SCREENSHOT,
+ ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK, ID_TIFF_JPG_PNG,
+ ID_VIEW_INTERPOLATED, ID_MODE_NAVIGATION, ID_ANALYZE_IMPORT, ID_NIFTI_IMPORT,
+ ID_PARREC_IMPORT, ID_MODE_DBS] = [wx.NewId() for number in range(21)]
 ID_EXIT = wx.ID_EXIT
 ID_ABOUT = wx.ID_ABOUT
@@ -161,6 +161,9 @@ class Slice(with_metaclass(utils.Singleton, object)):
         Publisher.subscribe(self.__show_current_mask, 'Show current mask')
         Publisher.subscribe(self.__clean_current_mask, 'Clean current mask')
+        Publisher.subscribe(self.__export_slice, 'Export slice')
+        Publisher.subscribe(self.__export_actual_mask, 'Export actual mask')
+
         Publisher.subscribe(self.__set_current_mask_threshold_limits,
                                         'Update threshold limits')
@@ -426,6 +429,23 @@ class Slice(with_metaclass(utils.Singleton, object)):
             session = ses.Session()
             session.ChangeProject()
+    def __export_slice(self, filename):
+        import h5py
+        f = h5py.File(filename, 'w')
+        f['data'] = self.matrix
+        f['spacing'] = self.spacing
+        f.flush()
+        f.close()
+
+    def __export_actual_mask(self, filename):
+        import h5py
+        f = h5py.File(filename, 'w')
+        self.do_threshold_to_all_slices()
+        f['data'] = self.current_mask.matrix[1:, 1:, 1:]
+        f['spacing'] = self.spacing
+        f.flush()
+        f.close()
+
     def create_temp_mask(self):
         temp_file = tempfile.mktemp()
         shape = self.matrix.shape
@@ -53,6 +53,15 @@ import invesalius.gui.preferences as preferences
 VIEW_TOOLS = [ID_LAYOUT, ID_TEXT] =\
                                 [wx.NewId() for number in range(2)]
+WILDCARD_EXPORT_SLICE = "HDF5 (*.hdf5)|*.hdf5|" \
+    "NIfTI 1 (*.nii)|*.nii|" \
+    "Compressed NIfTI (*.nii.gz)|*.nii.gz"
+
+IDX_EXT = {
+    0: '.hdf5',
+    1: '.nii',
+    2: '.nii.gz'
+}
 class MessageWatershed(wx.PopupWindow):
@@ -419,6 +428,8 @@ class Frame(wx.Frame):
                 self.SaveProject()
         elif id == const.ID_PROJECT_SAVE_AS:
             self.ShowSaveAsProject()
+        elif id == const.ID_EXPORT_SLICE:
+            self.ExportProject()
         elif id == const.ID_PROJECT_CLOSE:
             self.CloseProject()
         elif id == const.ID_EXIT:
@@ -629,6 +640,28 @@ class Frame(wx.Frame):
         """
         Publisher.sendMessage('Show save dialog', save_as=True)
+    def ExportProject(self):
+        """
+        Show save dialog to export slice.
+        """
+        p = prj.Project()
+
+        session = ses.Session()
+        last_directory = session.get('paths', 'last_directory_export_prj', '')
+        dlg = wx.FileDialog(None,
+                            "Export slice ...",
+                            last_directory, # last used directory
+                            os.path.split(p.name)[-1], # initial filename
+                            WILDCARD_EXPORT_SLICE,
+                            wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
+        if dlg.ShowModal() == wx.ID_OK:
+            filename = dlg.GetPath()
+            ext = IDX_EXT[dlg.GetFilterIndex()]
+            if not filename.endswith(ext):
+                filename += ext
+            p.export_project(filename)
+            session['paths']['last_directory_export_prj'] = os.path.split(filename)[0]
+
     def ShowBitmapImporter(self):
         """
         Tiff, BMP, JPEG and PNG
@@ -702,6 +735,7 @@ class MenuBar(wx.MenuBar):
         # not. Eg. save should only be available if a project is open
         self.enable_items = [const.ID_PROJECT_SAVE,
                              const.ID_PROJECT_SAVE_AS,
+                             const.ID_EXPORT_SLICE,
                              const.ID_PROJECT_CLOSE,
                              const.ID_REORIENT_IMG,
                              const.ID_FLOODFILL_MASK,
@@ -771,6 +805,7 @@ class MenuBar(wx.MenuBar):
         app(const.ID_PROJECT_OPEN, _("Open project...\tCtrl+O"))
         app(const.ID_PROJECT_SAVE, _("Save project\tCtrl+S"))
         app(const.ID_PROJECT_SAVE_AS, _("Save project as...\tCtrl+Shift+S"))
+        app(const.ID_EXPORT_SLICE, _("Export project"))
         app(const.ID_PROJECT_CLOSE, _("Close project"))
         file_menu.AppendSeparator()
         #app(const.ID_PROJECT_INFO, _("Project Information..."))
@@ -28,6 +28,7 @@ import sys
 import tarfile
 import tempfile
+import numpy as np
 import wx
 from wx.lib.pubsub import pub as Publisher
 import vtk
@@ -349,6 +350,70 @@ class Project(with_metaclass(Singleton, object)):
             measure.Load(measurements[index])
             self.measurement_dict[int(index)] = measure
+    def export_project(self, filename, save_masks=True):
+        if filename.lower().endswith('.hdf5') or filename.lower().endswith('.h5'):
+            self.export_project_to_hdf5(filename, save_masks)
+        elif filename.lower().endswith('.nii') or filename.lower().endswith('.nii.gz'):
+            self.export_project_to_nifti(filename, save_masks)
+
+    def export_project_to_hdf5(self, filename, save_masks=True):
+        import h5py
+        import invesalius.data.slice_ as slc
+        s = slc.Slice()
+        with h5py.File(filename, 'w') as f:
+            f['image'] = s.matrix
+            f['spacing'] = s.spacing
+
+            f["invesalius_version"] = const.INVESALIUS_VERSION
+            f["date"] = datetime.datetime.now().isoformat()
+            f["compress"] = self.compress
+            f["name"] = self.name # patient's name
+            f["modality"] = self.modality # CT, RMI, ...
+            f["orientation"] = self.original_orientation
+            f["window_width"] = self.window
+            f["window_level"] = self.level
+            f["scalar_range"] = self.threshold_range
+
+            if save_masks:
+                for index in self.mask_dict:
+                    mask = self.mask_dict[index]
+                    s.do_threshold_to_all_slices(mask)
+                    key = 'masks/{}'.format(index)
+                    f[key + '/name'] = mask.name
+                    f[key + '/matrix'] = mask.matrix[1:, 1:, 1:]
+                    f[key + '/colour'] = mask.colour[:3]
+                    f[key + '/opacity'] = mask.opacity
+                    f[key + '/threshold_range'] = mask.threshold_range
+                    f[key + '/edition_threshold_range'] = mask.edition_threshold_range
+                    f[key + '/visible'] = mask.is_shown
+                    f[key + '/edited'] = mask.was_edited
+
+    def export_project_to_nifti(self, filename, save_masks=True):
+        import invesalius.data.slice_ as slc
+        import nibabel as nib
+        s = slc.Slice()
+        img_nifti = nib.Nifti1Image(np.swapaxes(np.fliplr(s.matrix), 0, 2), None)
+        img_nifti.header.set_zooms(s.spacing)
+        img_nifti.header.set_dim_info(slice=0)
+        nib.save(img_nifti, filename)
+        if save_masks:
+            for index in self.mask_dict:
+                mask = self.mask_dict[index]
+                s.do_threshold_to_all_slices(mask)
+                mask_nifti = nib.Nifti1Image(np.swapaxes(np.fliplr(mask.matrix), 0, 2), None)
+                mask_nifti.header.set_zooms(s.spacing)
+                if filename.lower().endswith('.nii'):
+                    basename = filename[:-4]
+                    ext = filename[-4::]
+                elif filename.lower().endswith('.nii.gz'):
+                    basename = filename[:-7]
+                    ext = filename[-7::]
+                else:
+                    ext = '.nii'
+                    basename = filename
+                nib.save(mask_nifti, "{}_mask_{}_{}{}".format(basename, mask.index, mask.name, ext))
+
+
 def Compress(folder, filename, filelist, compress=False):
     tmpdir, tmpdir_ = os.path.split(folder)
     current_dir = os.path.abspath(".")
	@@ -336,6 +336,13 @@ def parse_comand_line():		@@ -336,6 +336,13 @@ def parse_comand_line():
336	parser.add_option("-a", "--export-to-all",	336	parser.add_option("-a", "--export-to-all",
337	help="Export to STL for all mask presets.")	337	help="Export to STL for all mask presets.")
338		338
		339	+ parser.add_option("--export-project",
		340	+ help="Export slices and mask to HDF5 or Nifti file.")
		341	+
		342	+ parser.add_option("--no-masks", action="store_false",
		343	+ dest="save_masks", default=True,
		344	+ help="Make InVesalius not export mask when exporting project.")
		345	+
339	options, args = parser.parse_args()	346	options, args = parser.parse_args()
340	return options, args	347	return options, args
341		348
	@@ -429,6 +436,17 @@ def check_for_export(options, suffix='', remove_surfaces=False):		@@ -429,6 +436,17 @@ def check_for_export(options, suffix='', remove_surfaces=False):
429	finally:	436	finally:
430	exit(0)	437	exit(0)
431		438
		439	+ if options.export_project:
		440	+ from invesalius.project import Project
		441	+ prj = Project()
		442	+ export_filename = options.export_project
		443	+ if suffix:
		444	+ export_filename, ext = os.path.splitext(export_filename)
		445	+ export_filename = u'{}-{}{}'.format(export_filename, suffix, ext)
		446	+
		447	+ prj.export_project(export_filename, save_masks=options.save_masks)
		448	+ print("Saved {}".format(export_filename))
		449	+
432		450
433	def export(path_, threshold_range, remove_surface=False):	451	def export(path_, threshold_range, remove_surface=False):
434	import invesalius.constants as const	452	import invesalius.constants as const
	@@ -161,6 +161,9 @@ class Slice(with_metaclass(utils.Singleton, object)):		@@ -161,6 +161,9 @@ class Slice(with_metaclass(utils.Singleton, object)):
161	Publisher.subscribe(self.__show_current_mask, 'Show current mask')	161	Publisher.subscribe(self.__show_current_mask, 'Show current mask')
162	Publisher.subscribe(self.__clean_current_mask, 'Clean current mask')	162	Publisher.subscribe(self.__clean_current_mask, 'Clean current mask')
163		163
		164	+ Publisher.subscribe(self.__export_slice, 'Export slice')
		165	+ Publisher.subscribe(self.__export_actual_mask, 'Export actual mask')
		166	+
164	Publisher.subscribe(self.__set_current_mask_threshold_limits,	167	Publisher.subscribe(self.__set_current_mask_threshold_limits,
165	'Update threshold limits')	168	'Update threshold limits')
166		169
	@@ -426,6 +429,23 @@ class Slice(with_metaclass(utils.Singleton, object)):		@@ -426,6 +429,23 @@ class Slice(with_metaclass(utils.Singleton, object)):
426	session = ses.Session()	429	session = ses.Session()
427	session.ChangeProject()	430	session.ChangeProject()
428		431
		432	+ def __export_slice(self, filename):
		433	+ import h5py
		434	+ f = h5py.File(filename, 'w')
		435	+ f['data'] = self.matrix
		436	+ f['spacing'] = self.spacing
		437	+ f.flush()
		438	+ f.close()
		439	+
		440	+ def __export_actual_mask(self, filename):
		441	+ import h5py
		442	+ f = h5py.File(filename, 'w')
		443	+ self.do_threshold_to_all_slices()
		444	+ f['data'] = self.current_mask.matrix[1:, 1:, 1:]
		445	+ f['spacing'] = self.spacing
		446	+ f.flush()
		447	+ f.close()
		448	+
429	def create_temp_mask(self):	449	def create_temp_mask(self):
430	temp_file = tempfile.mktemp()	450	temp_file = tempfile.mktemp()
431	shape = self.matrix.shape	451	shape = self.matrix.shape
	@@ -53,6 +53,15 @@ import invesalius.gui.preferences as preferences		@@ -53,6 +53,15 @@ import invesalius.gui.preferences as preferences
53	VIEW_TOOLS = [ID_LAYOUT, ID_TEXT] =\	53	VIEW_TOOLS = [ID_LAYOUT, ID_TEXT] =\
54	[wx.NewId() for number in range(2)]	54	[wx.NewId() for number in range(2)]
55		55
		56	+WILDCARD_EXPORT_SLICE = "HDF5 (.hdf5)\|.hdf5\|" \
		57	+ "NIfTI 1 (.nii)\|.nii\|" \
		58	+ "Compressed NIfTI (.nii.gz)\|.nii.gz"
		59	+
		60	+IDX_EXT = {
		61	+ 0: '.hdf5',
		62	+ 1: '.nii',
		63	+ 2: '.nii.gz'
		64	+}
56		65
57		66
58	class MessageWatershed(wx.PopupWindow):	67	class MessageWatershed(wx.PopupWindow):
	@@ -419,6 +428,8 @@ class Frame(wx.Frame):		@@ -419,6 +428,8 @@ class Frame(wx.Frame):
419	self.SaveProject()	428	self.SaveProject()
420	elif id == const.ID_PROJECT_SAVE_AS:	429	elif id == const.ID_PROJECT_SAVE_AS:
421	self.ShowSaveAsProject()	430	self.ShowSaveAsProject()
		431	+ elif id == const.ID_EXPORT_SLICE:
		432	+ self.ExportProject()
422	elif id == const.ID_PROJECT_CLOSE:	433	elif id == const.ID_PROJECT_CLOSE:
423	self.CloseProject()	434	self.CloseProject()
424	elif id == const.ID_EXIT:	435	elif id == const.ID_EXIT:
	@@ -629,6 +640,28 @@ class Frame(wx.Frame):		@@ -629,6 +640,28 @@ class Frame(wx.Frame):
629	"""	640	"""
630	Publisher.sendMessage('Show save dialog', save_as=True)	641	Publisher.sendMessage('Show save dialog', save_as=True)
631		642
		643	+ def ExportProject(self):
		644	+ """
		645	+ Show save dialog to export slice.
		646	+ """
		647	+ p = prj.Project()
		648	+
		649	+ session = ses.Session()
		650	+ last_directory = session.get('paths', 'last_directory_export_prj', '')
		651	+ dlg = wx.FileDialog(None,
		652	+ "Export slice ...",
		653	+ last_directory, # last used directory
		654	+ os.path.split(p.name)[-1], # initial filename
		655	+ WILDCARD_EXPORT_SLICE,
		656	+ wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
		657	+ if dlg.ShowModal() == wx.ID_OK:
		658	+ filename = dlg.GetPath()
		659	+ ext = IDX_EXT[dlg.GetFilterIndex()]
		660	+ if not filename.endswith(ext):
		661	+ filename += ext
		662	+ p.export_project(filename)
		663	+ session['paths']['last_directory_export_prj'] = os.path.split(filename)[0]
		664	+
632	def ShowBitmapImporter(self):	665	def ShowBitmapImporter(self):
633	"""	666	"""
634	Tiff, BMP, JPEG and PNG	667	Tiff, BMP, JPEG and PNG
	@@ -702,6 +735,7 @@ class MenuBar(wx.MenuBar):		@@ -702,6 +735,7 @@ class MenuBar(wx.MenuBar):
702	# not. Eg. save should only be available if a project is open	735	# not. Eg. save should only be available if a project is open
703	self.enable_items = [const.ID_PROJECT_SAVE,	736	self.enable_items = [const.ID_PROJECT_SAVE,
704	const.ID_PROJECT_SAVE_AS,	737	const.ID_PROJECT_SAVE_AS,
		738	+ const.ID_EXPORT_SLICE,
705	const.ID_PROJECT_CLOSE,	739	const.ID_PROJECT_CLOSE,
706	const.ID_REORIENT_IMG,	740	const.ID_REORIENT_IMG,
707	const.ID_FLOODFILL_MASK,	741	const.ID_FLOODFILL_MASK,
	@@ -771,6 +805,7 @@ class MenuBar(wx.MenuBar):		@@ -771,6 +805,7 @@ class MenuBar(wx.MenuBar):
771	app(const.ID_PROJECT_OPEN, _("Open project...\tCtrl+O"))	805	app(const.ID_PROJECT_OPEN, _("Open project...\tCtrl+O"))
772	app(const.ID_PROJECT_SAVE, _("Save project\tCtrl+S"))	806	app(const.ID_PROJECT_SAVE, _("Save project\tCtrl+S"))
773	app(const.ID_PROJECT_SAVE_AS, _("Save project as...\tCtrl+Shift+S"))	807	app(const.ID_PROJECT_SAVE_AS, _("Save project as...\tCtrl+Shift+S"))
		808	+ app(const.ID_EXPORT_SLICE, _("Export project"))
774	app(const.ID_PROJECT_CLOSE, _("Close project"))	809	app(const.ID_PROJECT_CLOSE, _("Close project"))
775	file_menu.AppendSeparator()	810	file_menu.AppendSeparator()
776	#app(const.ID_PROJECT_INFO, _("Project Information..."))	811	#app(const.ID_PROJECT_INFO, _("Project Information..."))
	@@ -28,6 +28,7 @@ import sys		@@ -28,6 +28,7 @@ import sys
28	import tarfile	28	import tarfile
29	import tempfile	29	import tempfile
30		30
		31	+import numpy as np
31	import wx	32	import wx
32	from wx.lib.pubsub import pub as Publisher	33	from wx.lib.pubsub import pub as Publisher
33	import vtk	34	import vtk
	@@ -349,6 +350,70 @@ class Project(with_metaclass(Singleton, object)):		@@ -349,6 +350,70 @@ class Project(with_metaclass(Singleton, object)):
349	measure.Load(measurements[index])	350	measure.Load(measurements[index])
350	self.measurement_dict[int(index)] = measure	351	self.measurement_dict[int(index)] = measure
351		352
		353	+ def export_project(self, filename, save_masks=True):
		354	+ if filename.lower().endswith('.hdf5') or filename.lower().endswith('.h5'):
		355	+ self.export_project_to_hdf5(filename, save_masks)
		356	+ elif filename.lower().endswith('.nii') or filename.lower().endswith('.nii.gz'):
		357	+ self.export_project_to_nifti(filename, save_masks)
		358	+
		359	+ def export_project_to_hdf5(self, filename, save_masks=True):
		360	+ import h5py
		361	+ import invesalius.data.slice_ as slc
		362	+ s = slc.Slice()
		363	+ with h5py.File(filename, 'w') as f:
		364	+ f['image'] = s.matrix
		365	+ f['spacing'] = s.spacing
		366	+
		367	+ f["invesalius_version"] = const.INVESALIUS_VERSION
		368	+ f["date"] = datetime.datetime.now().isoformat()
		369	+ f["compress"] = self.compress
		370	+ f["name"] = self.name # patient's name
		371	+ f["modality"] = self.modality # CT, RMI, ...
		372	+ f["orientation"] = self.original_orientation
		373	+ f["window_width"] = self.window
		374	+ f["window_level"] = self.level
		375	+ f["scalar_range"] = self.threshold_range
		376	+
		377	+ if save_masks:
		378	+ for index in self.mask_dict:
		379	+ mask = self.mask_dict[index]
		380	+ s.do_threshold_to_all_slices(mask)
		381	+ key = 'masks/{}'.format(index)
		382	+ f[key + '/name'] = mask.name
		383	+ f[key + '/matrix'] = mask.matrix[1:, 1:, 1:]
		384	+ f[key + '/colour'] = mask.colour[:3]
		385	+ f[key + '/opacity'] = mask.opacity
		386	+ f[key + '/threshold_range'] = mask.threshold_range
		387	+ f[key + '/edition_threshold_range'] = mask.edition_threshold_range
		388	+ f[key + '/visible'] = mask.is_shown
		389	+ f[key + '/edited'] = mask.was_edited
		390	+
		391	+ def export_project_to_nifti(self, filename, save_masks=True):
		392	+ import invesalius.data.slice_ as slc
		393	+ import nibabel as nib
		394	+ s = slc.Slice()
		395	+ img_nifti = nib.Nifti1Image(np.swapaxes(np.fliplr(s.matrix), 0, 2), None)
		396	+ img_nifti.header.set_zooms(s.spacing)
		397	+ img_nifti.header.set_dim_info(slice=0)
		398	+ nib.save(img_nifti, filename)
		399	+ if save_masks:
		400	+ for index in self.mask_dict:
		401	+ mask = self.mask_dict[index]
		402	+ s.do_threshold_to_all_slices(mask)
		403	+ mask_nifti = nib.Nifti1Image(np.swapaxes(np.fliplr(mask.matrix), 0, 2), None)
		404	+ mask_nifti.header.set_zooms(s.spacing)
		405	+ if filename.lower().endswith('.nii'):
		406	+ basename = filename[:-4]
		407	+ ext = filename[-4::]
		408	+ elif filename.lower().endswith('.nii.gz'):
		409	+ basename = filename[:-7]
		410	+ ext = filename[-7::]
		411	+ else:
		412	+ ext = '.nii'
		413	+ basename = filename
		414	+ nib.save(mask_nifti, "{}_mask_{}_{}{}".format(basename, mask.index, mask.name, ext))
		415	+
		416	+
352	def Compress(folder, filename, filelist, compress=False):	417	def Compress(folder, filename, filelist, compress=False):
353	tmpdir, tmpdir_ = os.path.split(folder)	418	tmpdir, tmpdir_ = os.path.split(folder)
354	current_dir = os.path.abspath(".")	419	current_dir = os.path.abspath(".")