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	336	parser.add_option("-a", "--export-to-all",
337	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	346	options, args = parser.parse_args()
340	347	return options, args
341	348
...	...	@@ -429,6 +436,17 @@ def check_for_export(options, suffix='', remove_surfaces=False):
429	436	finally:
430	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	451	def export(path_, threshold_range, remove_surface=False):
434	452	import invesalius.constants as const
...	...
...	...	@@ -506,10 +506,11 @@ VTK_WARNING = 0
506	506	#----------------------------------------------------------
507	507
508	508	[ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,
509		-ID_PROJECT_CLOSE, ID_PROJECT_INFO, ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET,
510		-ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK,
511		-ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED, ID_MODE_NAVIGATION, ID_ANALYZE_IMPORT,
512		-ID_NIFTI_IMPORT, ID_PARREC_IMPORT, ID_MODE_DBS] = [wx.NewId() for number in range(19)]
	509	+ ID_PROJECT_CLOSE, ID_EXPORT_SLICE, ID_EXPORT_MASK, ID_PROJECT_INFO,
	510	+ ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET, ID_PRINT_SCREENSHOT,
	511	+ ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK, ID_TIFF_JPG_PNG,
	512	+ ID_VIEW_INTERPOLATED, ID_MODE_NAVIGATION, ID_ANALYZE_IMPORT, ID_NIFTI_IMPORT,
	513	+ ID_PARREC_IMPORT, ID_MODE_DBS] = [wx.NewId() for number in range(21)]
513	514	ID_EXIT = wx.ID_EXIT
514	515	ID_ABOUT = wx.ID_ABOUT
515	516
...	...
...	...	@@ -161,6 +161,9 @@ class Slice(with_metaclass(utils.Singleton, object)):
161	161	Publisher.subscribe(self.__show_current_mask, 'Show current mask')
162	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	167	Publisher.subscribe(self.__set_current_mask_threshold_limits,
165	168	'Update threshold limits')
166	169
...	...	@@ -426,6 +429,23 @@ class Slice(with_metaclass(utils.Singleton, object)):
426	429	session = ses.Session()
427	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	449	def create_temp_mask(self):
430	450	temp_file = tempfile.mktemp()
431	451	shape = self.matrix.shape
...	...
...	...	@@ -53,6 +53,15 @@ import invesalius.gui.preferences as preferences
53	53	VIEW_TOOLS = [ID_LAYOUT, ID_TEXT] =\
54	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	67	class MessageWatershed(wx.PopupWindow):
...	...	@@ -419,6 +428,8 @@ class Frame(wx.Frame):
419	428	self.SaveProject()
420	429	elif id == const.ID_PROJECT_SAVE_AS:
421	430	self.ShowSaveAsProject()
	431	+ elif id == const.ID_EXPORT_SLICE:
	432	+ self.ExportProject()
422	433	elif id == const.ID_PROJECT_CLOSE:
423	434	self.CloseProject()
424	435	elif id == const.ID_EXIT:
...	...	@@ -629,6 +640,28 @@ class Frame(wx.Frame):
629	640	"""
630	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	665	def ShowBitmapImporter(self):
633	666	"""
634	667	Tiff, BMP, JPEG and PNG
...	...	@@ -702,6 +735,7 @@ class MenuBar(wx.MenuBar):
702	735	# not. Eg. save should only be available if a project is open
703	736	self.enable_items = [const.ID_PROJECT_SAVE,
704	737	const.ID_PROJECT_SAVE_AS,
	738	+ const.ID_EXPORT_SLICE,
705	739	const.ID_PROJECT_CLOSE,
706	740	const.ID_REORIENT_IMG,
707	741	const.ID_FLOODFILL_MASK,
...	...	@@ -771,6 +805,7 @@ class MenuBar(wx.MenuBar):
771	805	app(const.ID_PROJECT_OPEN, _("Open project...\tCtrl+O"))
772	806	app(const.ID_PROJECT_SAVE, _("Save project\tCtrl+S"))
773	807	app(const.ID_PROJECT_SAVE_AS, _("Save project as...\tCtrl+Shift+S"))
	808	+ app(const.ID_EXPORT_SLICE, _("Export project"))
774	809	app(const.ID_PROJECT_CLOSE, _("Close project"))
775	810	file_menu.AppendSeparator()
776	811	#app(const.ID_PROJECT_INFO, _("Project Information..."))
...	...
...	...	@@ -28,6 +28,7 @@ import sys
28	28	import tarfile
29	29	import tempfile
30	30
	31	+import numpy as np
31	32	import wx
32	33	from wx.lib.pubsub import pub as Publisher
33	34	import vtk
...	...	@@ -349,6 +350,70 @@ class Project(with_metaclass(Singleton, object)):
349	350	measure.Load(measurements[index])
350	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	417	def Compress(folder, filename, filelist, compress=False):
353	418	tmpdir, tmpdir_ = os.path.split(folder)
354	419	current_dir = os.path.abspath(".")
...	...