Update dvc v26

.gitignore

@@ -3,3 +3,4 @@ docs/build/*
 docs/source/_build/*
 src/idvc/version.py
 build/*
+*.profraw

README.md

@@ -11,3 +11,21 @@ iDVC depends on code initially developed by Prof. Brian K. Bay and collaborators
 [1] B. K. Bay, T. S. Smith, D. P. Fyhrie, M. Saad "Digital volume correlation: Three-dimensional strain mapping using x-ray tomography", *Experimental Mechanics* **39** 217–226, 1999. [DOI: 10.1007/BF02323555](https://doi.org/10.1007/BF02323555)
 
 [2] B. K. Bay "Methods and applications of digital volume correlation", *J. Strain Analysis* **43** 745-760, 2008. [DOI: 10.1243/03093247JSA436](https://doi.org/10.1243/03093247JSA436)
+
+
+# MacOS + Qt + VTK
+
+`conda-forge`'s VTK package depends on Qt6 and we only tested this app with Qt5. On MacOS this seems to be a problem as the OS finds 2 files which provide the same functionality so it raises an error and nothing works. The suggested workaround is to install the CILViewer (from the repo), `PySide2` (`conda-forge`) and [VTK](https://docs.vtk.org/en/latest/advanced/available_python_wheels.html) (from Kitware's wheels) manually.
+
+
+```bash
+pip install --extra-index-url https://wheels.vtk.org vtk
+```
+
+```yaml
+dependencies:
+  - pip
+  - pip:
+    - --extra-index-url https://wheels.vtk.org
+    - vtk
+```

recipe/dev_environment.yml

@@ -11,10 +11,11 @@ dependencies:
     - pyside2
     - scipy
     - ccpi::ccpi-viewer >=25.0.0
-    - ccpi::ccpi-dvc >=22.0.0
+    - ccpi/label/dev::ccpi-dvc >=25.0.0
     - natsort
     - docopt
     - matplotlib
     - openmp                # [osx]
     - qdarkstyle
     - vtk
+    - filetype

recipe/dev_environment_osx.yml

@@ -0,0 +1,29 @@
+name: idvc_dev
+channels:
+  - conda-forge
+  - ccpi
+dependencies:
+    # - eqt >=1.0.1
+    - openpyxl
+    - python
+    - numpy
+    - pandas
+    - pyside2
+    - scipy
+    # - ccpi::ccpi-viewer >=25.0.0
+    - ccpi/label/dev::ccpi-dvc >=25.0.0
+    - natsort
+    - docopt
+    - matplotlib
+    - llvm-openmp                
+    - qdarkstyle
+    - h5py
+    - pyyaml
+    - schema
+    - qtpy
+    - filetype
+    - pip:
+      - --extra-index-url https://wheels.vtk.org
+      - vtk
+      - git+https://github.com/TomographicImaging/CILViewer.git#subdirectory=Wrappers/Python
+      - eqt >=1.0.1

recipe/meta.yaml

@@ -41,8 +41,8 @@ requirements:
     - pandas
     - pyside2
     - scipy
-    - ccpi-viewer >=25.0.0
-    - ccpi-dvc >=22.0.0
+    - ccpi::ccpi-viewer >=25.0.0
+    - ccpi/label/dev::ccpi-dvc >=25.0.0
     - natsort
     - docopt
     - matplotlib

src/idvc/dvc_config_template.txt

@@ -42,8 +42,8 @@ min_vol_fract	{min_vol_fract}			### only search if subvol fraction is greater th
 disp_max		{disp_max}			### in voxels, used for range checking and global search limits
 num_srch_dof		{num_srch_dof}			### 3, 6, or 12
 obj_function		{obj_function}			### sad, ssd, zssd, nssd, znssd 
-interp_type		{interp_type}		### trilinear, tricubic
-
+interp_type		{interp_type}		### trilinear, tricubic, tri_bspline_3, tri_bspline_5, tri_bspline_7
+{bspline_order}
 ### optional parameters tuning and refining the search process
 
 rigid_trans		{rigid_trans}		### rigid body offset of target volume, in voxels

src/idvc/dvc_interface.py

@@ -54,7 +54,7 @@
 from ccpi.viewer.utils.colormaps import CILColorMaps
 
 from natsort import natsorted
-import imghdr
+import filetype
 import glob
 
 # from vtk.numpy_interface import algorithms as algs
@@ -762,8 +762,9 @@ def copy_file(self, start_location, end_location, image_var, **kwargs):
             N = len(start_location)
             for i,fs in enumerate(zip(start_location, end_location)):
                 if N > 1:
-                    ftype = imghdr.what(fs[0])
-                    if ftype != 'tiff':
+                    kind = filetype.guess(fs[0])
+                    ftype = kind.extension if kind is not None else ""
+                    if ftype not in ['tiff', 'tif']:
                         raise ValueError('File type not supported: {}'.format(fs[0]))
                 progress_callback.emit(i/N*100)
                 shutil.copyfile(fs[0], fs[1])
@@ -4384,6 +4385,9 @@ def CreateRunDVCPanel(self):
         rdvc_widgets['run_iterp_type_entry'].addItem('Nearest')
         rdvc_widgets['run_iterp_type_entry'].addItem('Trilinear')
         rdvc_widgets['run_iterp_type_entry'].addItem('Tricubic')
+        rdvc_widgets['run_iterp_type_entry'].addItem('tri_bspline_3')
+        rdvc_widgets['run_iterp_type_entry'].addItem('tri_bspline_5')
+        rdvc_widgets['run_iterp_type_entry'].addItem('tri_bspline_7')
         rdvc_widgets['run_iterp_type_entry'].setCurrentIndex(2)
         rdvc_widgets['run_iterp_type_entry'].setToolTip(interp_text)
         formLayout.setWidget(widgetno, QFormLayout.FieldRole, rdvc_widgets['run_iterp_type_entry'])
@@ -4753,15 +4757,15 @@ def create_run_config(self, **kwargs):
             run_config['subvol_geom'] = self.pointcloud_parameters['pointcloud_volume_shape_entry'].currentText().lower()
             run_config['subvol_npts'] = self.subvolume_points
 
-            run_config['disp_max'] = self.rdvc_widgets['run_max_displacement_entry'].value(), #38 for test image
+            run_config['step_max'] = self.rdvc_widgets['run_max_displacement_entry'].value(), #38 for test image
             run_config['dof'] = self.rdvc_widgets['run_ndof_entry'].currentText()
             run_config['obj'] = self.rdvc_widgets['run_objf_entry'].currentText()
             run_config['interp_type'] = self.rdvc_widgets['run_iterp_type_entry'].currentText().lower()
 
             if (hasattr(self, 'translate')):
-                run_config['rigid_trans'] = str(self.translate.GetTranslation()[0]*-1) + " " + str(self.translate.GetTranslation()[1]*-1) + " " + str(self.translate.GetTranslation()[2]*-1)
+                run_config['start_estimate'] = str(self.translate.GetTranslation()[0]*-1) + " " + str(self.translate.GetTranslation()[1]*-1) + " " + str(self.translate.GetTranslation()[2]*-1)
             else:
-                run_config['rigid_trans']= "0.0 0.0 0.0"
+                run_config['start_estimate']= "0.0 0.0 0.0"
 
             self.run_folder = "Results/" + folder_name
             run_config['run_folder'] = self.run_folder
@@ -5006,7 +5010,7 @@ def CreateViewDVCResultsPanel(self):
 
         scroll_area = dockWidget.widget()
         scroll_area.apply_qdarkstyle_to_buttons(self.dvc_results_panel[1])
-
+        
     def show_run_pcs(self):
         #show pointcloud files in list
         self.result_widgets['pc_entry'].clear()
@@ -5040,16 +5044,16 @@ def LoadResultsOnViewer(self):
             try:
                 subvol_size = int(self.result_widgets['pc_entry'].currentText())
             except ValueError as ve:
-                self.warningDialog("Invalid input at Subvolume Size", "Error")
+                self.warningDialog(message="Invalid input at Subvolume Size", window_title="Parse Error", detailed_text=f"{ve}")
                 return
             try:
                 subvol_points = int(self.result_widgets['subvol_entry'].currentText())
             except ValueError as ve:
-                self.warningDialog("Invalid input at Subvolume Size", "Error")
+                self.warningDialog(message="Invalid input at Subvolume Entry", window_title="Parse Error", detailed_text=f"{ve}")
                 return
 
             if(subvol_points == ""):
-                self.warningDialog("An error occurred with this run so the results could not be displayed.", "Error")
+                self.warningDialog(message="An error occurred with this run so the results could not be displayed.", window_title="Error")
                 return
 
 

src/idvc/dvc_runner.py

@@ -32,25 +32,16 @@ def emit(self, *args, **kwargs):
 count = 0
 runs_completed = 0
 
-blank_config = '''###############################################################################
-#																	
-#
-#		example dvc process control file		
-#
-#
-###############################################################################
-
-# all lines beginning with a # character are ignored
-# some parameters are conditionally required, depending on the setting of other parameters
-# for example, if subvol_thresh is off, the threshold description parameters are not required
-
+blank_config = '''
 ### file names
 
-reference_filename	{reference_filename}		### reference tomography image volume
-correlate_filename	{correlate_filename}		### correlation tomography image volume
+reference_filename	{reference_filename}		### single raster file (raw) of same dimensions as the correlate_volume
+correlate_filename	{correlate_filename}		### single raster file (raw) of same dimensions as the reference_volume
+
+point_cloud_filename	{point_cloud_filename}	### tab/space/comma delimited text file with point cloud labels (n) and (xyz) locations
+output_filename		{output_filename}		### base name for run status (.stat) and displacement data (.disp) output files
 
-point_cloud_filename	{point_cloud_filename}	### file of search point locations
-output_filename		{output_filename}		### base name for output files
+num_points_to_process   {num_points_to_process}  ### Number of points in the point cloud to process
 
 ### description of the image data files, all must be the same size and structure
 
@@ -59,33 +50,35 @@ def emit(self, *args, **kwargs):
 vol_wide		{vol_wide}			### width in pixels of each slice
 vol_high		{vol_high}			### height in pixels of each slice
 vol_tall		{vol_tall}			### number of slices in the stack
-vol_endian		{vol_endian}        ### big or little endian byte ordering
+vol_endian		{vol_endian}        ### big or little endian byte ordering, ignored if vol_bit_depth is 8
 
 ### parameters defining the subvolumes that will be created at each search point
 
-subvol_geom		{subvol_geom}			### cube, sphere
+subvol_geom		{subvol_geom}			### cube, sphere: geometry of the subvolumes
 subvol_size		{subvol_size}			### side length or diameter, in voxels
 subvol_npts		{subvol_npts}			### number of points to distribute within the subvol
+subvol_aspect	{subvol_aspect}	### stretch or contract the subvolume in any coordinate direction between 0.5 and 2.0
 
-subvol_thresh		{subvol_thresh}			### on or off, evaluate subvolumes based on threshold
-gray_thresh_min		{gray_thresh_min}			### lower limit of a gray threshold range if subvol_thresh is on
-gray_thresh_max		{gray_thresh_max}			### upper limit of a gray threshold range if subvol_thresh is on
-min_vol_fract		{min_vol_fract}			### only search if subvol fraction is greater than
-
-### required parameters defining the basic the search process
+###
+###	 Keywords in group opt_mthd
+###
 
-disp_max		{disp_max}			### in voxels, used for range checking and global search limits
-num_srch_dof		{num_srch_dof}			### 3, 6, or 12
-obj_function		{obj_function}			### sad, ssd, zssd, nssd, znssd 
-interp_type		{interp_type}		### trilinear, tricubic
+num_srch_dof	{num_srch_dof}	### 3 (translation), 6 (+rotation), or 12 (+strain)
+obj_function		{obj_function}			### ssd, zssd, nssd, znssd 
+interp_type		{interp_type}	### trilinear tricubic tri_bspline_3 tri_bspline_5 tri_bspline_7
+start_position	{starting_point}	### x,y,z location of starting point for DVC analysisstart_estimate 
+start_estimate	{start_estimate}	### x,y,z displacement (u,v,w) in voxels at the start_position
+step_max		{step_max}	### maximum parameter step allowed during optimization, see also step_tol
 
 ### optional parameters tuning and refining the search process
 
-rigid_trans		{rigid_trans}		### rigid body offset of target volume, in voxels
-basin_radius		{basin_radius}			### coarse-search resolution, in voxels, 0.0 = none
-subvol_aspect		{subvol_aspect}		### subvolume aspect ratio
-num_points_to_process   {num_points_to_process}  ### Number of points in the point cloud to process
-starting_point  {starting_point}    ### x,y,z location of starting point for DVC analysis
+###
+###	 Keywords in group opt_tune
+###
+
+# cost_tol	1.0e-06	### optional tuning of objective function convergence tolerance
+# step_tol	1.0e-04	### optional tuning of parameter vector convergence tolerance
+# max_iter	20	### optional change in the maximum number of optimization iterations
 '''
 
 def update_progress(main_window, process, total_points, required_runs, run_succeeded, start_time, num_points_to_process):
@@ -232,7 +225,8 @@ def set_up(self, *args, **kwargs):
         - disp_max: maximum displacement in voxels
         - dof: number of parameters in the optimisation, 3,6, or 12
         - obj: objective function, either sad, ssd, zssd, nssd, or znssd
-        - interp_type: interpolation type, either trilinear or tricubic
+        - interp_type: interpolation type, either trilinear, tricubic, or bspline
+        - bspline_order: order of the B-spline interpolation, only used if interp_type is bspline
         - run_folder: folder to save the run results and configurations
         - rigid_trans: rigid translation between the reference and correlation volumes
         - point0_world_coordinate: world coordinates of the starting point for the DVC analysis
@@ -314,13 +308,13 @@ def set_up(self, *args, **kwargs):
 
         subvol_npts = config['subvol_npts']
 
-        disp_max = int(config['disp_max'][0]) #TODO: need to change
+        step_max = int(config['step_max'][0]) #TODO: need to change
         dof = int(config['dof'])
         obj = config['obj']
         interp_type = config['interp_type']
 
-        rigid_trans = config['rigid_trans']
-        starting_point = config['point0_world_coordinate']
+        start_estimate = config['start_estimate']
+        start_position = config['point0_world_coordinate']
 
         # Change directory into the folder where the run will be saved:
         os.chdir(self.session_folder)
@@ -394,33 +388,29 @@ def set_up(self, *args, **kwargs):
                     return
 
 
+
                 config =  blank_config.format(
-                    reference_filename=  reference_file, # reference tomography image volume
-                    correlate_filename=  correlate_file, # correlation tomography image volume
+                    reference_filename=    reference_file, # reference tomography image volume
+                    correlate_filename=    correlate_file, # correlation tomography image volume
                     point_cloud_filename = grid_roi_fname,
-                    output_filename= output_filename,
+                    output_filename=       output_filename,
                     vol_bit_depth=  vol_bit_depth, # get from ref, 8 or 16
-                    vol_hdr_lngth=vol_hdr_lngth,# get from ref, fixed-length header size, may be zero
-                    vol_wide= dims[0], # number of x slices
-                    vol_high= dims[1], # number of y slices
-                    vol_tall= dims[2], #number of z slices
-                    vol_endian = endian,
-                    subvol_geom=  subvol_geom,
-                    subvol_size=  subvolume_size, 
-                    subvol_npts= subvolume_point,
-                    subvol_thresh='off',
-                    gray_thresh_min='27',
-                    gray_thresh_max='127',
-                    min_vol_fract='0.2',
-                    disp_max=  disp_max, #38 for test image
-                    num_srch_dof=  dof, #6 for test image
-                    obj_function=  obj, 
-                    interp_type=  interp_type, #tricubic for test image
-                    rigid_trans= rigid_trans, #translation between ref and cor - determined from image registration
-                    basin_radius='0.0',
+                    vol_hdr_lngth=  vol_hdr_lngth,# get from ref, fixed-length header size, may be zero
+                    vol_wide=       dims[0], # number of x slices
+                    vol_high=       dims[1], # number of y slices
+                    vol_tall=       dims[2], #number of z slices
+                    vol_endian =    endian,
+                    subvol_geom=    subvol_geom,
+                    subvol_size=    subvolume_size, 
+                    subvol_npts=    subvolume_point,
+                    step_max=       step_max, #38 for test image
+                    num_srch_dof=   dof, #6 for test image
+                    obj_function=   obj, 
+                    interp_type=    interp_type, #tricubic for test image
+                    start_estimate=    start_estimate, #translation between ref and cor - determined from image registration
                     subvol_aspect='1.0 1.0 1.0',# image spacing
                     num_points_to_process=num_points_to_process, 
-                    starting_point='{} {} {}'.format(*starting_point)) 
+                    starting_point='{} {} {}'.format(*start_position)) 
                 time.sleep(1)
                 with open(config_filename,"w") as config_file:
                     config_file.write(config)

src/idvc/io.py

@@ -13,7 +13,7 @@
 #   Author: Laura Murgatroyd (UKRI-STFC)
 #   Author: Edoardo Pasca (UKRI-STFC)
 
-import imghdr
+import filetype
 import os
 import shutil
 import sys
@@ -116,7 +116,8 @@ def getFileExtension(self):
             file_extension = os.path.splitext(self.image)[1]
         else:
             for image in self.image_files:
-                file_extension = imghdr.what(image)
+                kind = filetype.guess(image)
+                file_extension = kind.extension if kind is not None else ""
                 if file_extension.lower() not in ['tiff', 'tif']:
                     error_title = "Read Error"
                     error_text = "Error reading file: ({filename})".format(