Export slices mask (invesalius#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

app.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='', 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

invesalius/constants.py

@@ -506,10 +506,11 @@
 #----------------------------------------------------------
 
 [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
 

invesalius/data/slice_.py

@@ -161,6 +161,9 @@ def __bind_events(self):
         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 @@ def __clean_current_mask(self):
             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

invesalius/gui/frame.py

@@ -53,6 +53,15 @@
 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 @@ def OnMenuClick(self, evt):
                 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 @@ def ShowSaveAsProject(self):
         """
         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 @@ def __init__(self, parent):
         # 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 @@ def __init_items(self):
         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..."))

invesalius/project.py

@@ -28,6 +28,7 @@
 import tarfile
 import tempfile
 
+import numpy as np
 import wx
 from wx.lib.pubsub import pub as Publisher
 import vtk
@@ -349,6 +350,70 @@ def OpenPlistProject(self, filename):
             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(".")