pyvale 2025.5.3__cp311-cp311-macosx_13_0_x86_64.whl

pyvale/imagedef2d.py

@@ -0,0 +1,569 @@
+# ==============================================================================
+# pyvale: the python validation engine
+# License: MIT
+# Copyright (C) 2025 The Computer Aided Validation Team
+# ==============================================================================
+
+"""
+NOTE: This module is a feature under developement.
+"""
+
+import time
+import warnings
+from dataclasses import dataclass
+from pathlib import Path
+import numpy as np
+from scipy.interpolate import griddata
+from scipy.interpolate import RectBivariateSpline
+from scipy import ndimage
+
+from pyvale.rasternp import edge_function, RasterNP
+from pyvale.cameradata2d import CameraData2D
+from pyvale.cameratools import CameraTools
+
+
+@dataclass(slots=True)
+class ImageDefOpts:
+    save_path: Path | None = None
+    save_tag: str = "defimage"
+
+    mask_input_image: bool = True
+
+    crop_on: bool = False
+    crop_px: np.ndarray | None = None # only used to crop input image if above is true
+
+    calc_res_from_fe: bool =  False
+    calc_res_border_px: int = 5
+
+    add_static_ref: bool = False
+
+    fe_interp: str = "linear"
+    fe_rescale: bool = True
+    fe_extrap_outside_fov: bool = True # forces displacements outside the
+    #subsample: int = 2 # MOVED TO CAMERA DATA
+
+    image_def_order: int = 3
+    image_def_extrap: str = "nearest"
+    image_def_extval: float = 0.0 # only used if above is "constant"
+
+    def_complex_geom: bool = True
+
+    def __post_init__(self) -> None:
+        if self.save_path is None:
+            self.save_path = Path.cwd() / "deformed_images"
+
+
+class ImageDef2D:
+
+    @staticmethod
+    def image_mask_from_sim(cam_data: CameraData2D,
+                            image: np.ndarray,
+                            coords: np.ndarray,
+                            connectivity: np.ndarray
+                            ) -> tuple[np.ndarray,np.ndarray]:
+
+        # Here to allow for addition
+        #subsample: int = cam_data.subsample
+        subsample: int = 1
+
+        coords_raster = coords - cam_data.roi_cent_world
+        if coords_raster.shape[1] >= 3:
+            coords_raster = coords_raster[:,:-1]
+
+        # Coords NDC: Convert to normalised device coords in the range [-1,1]
+        coords_raster[:,0] = 2*coords_raster[:,0] / cam_data.field_of_view[0]
+        coords_raster[:,1] = 2*coords_raster[:,1] / cam_data.field_of_view[1]
+
+        # Coords Raster: Covert to pixel (raster) coords
+        # Shape = ([X,Y,Z],num_nodes)
+        coords_raster[:,0] = (coords_raster[:,0] + 1)/2 * cam_data.pixels_count[0]
+        coords_raster[:,1] = (1-coords_raster[:,1])/2 * cam_data.pixels_count[1]
+
+        # shape=(num_elems,node_per_elem,coord[x,y])
+        elem_coords = np.ascontiguousarray(coords_raster[connectivity,:])
+
+        #shape=(num_elems,coord[x,y,z])
+        elem_coord_min = np.min(elem_coords,axis=1)
+        elem_coord_max = np.max(elem_coords,axis=1)
+
+        # Check that min/max nodes are within the 4 edges of the camera image
+        #shape=(4_edges_to_check,num_elems)
+        crop_mask = np.zeros([elem_coords.shape[0],4],dtype=np.int8)
+        crop_mask[elem_coord_min[:,0] <= (cam_data.pixels_count[0]-1), 0] = 1
+        crop_mask[elem_coord_min[:,1] <= (cam_data.pixels_count[1]-1), 1] = 1
+        crop_mask[elem_coord_max[:,0] >= 0, 2] = 1
+        crop_mask[elem_coord_max[:,1] >= 0, 3] = 1
+        crop_mask = np.sum(crop_mask,axis=1) == 4
+
+        # Mask the element coords
+        elem_coords =  np.ascontiguousarray(elem_coords[crop_mask,:,:])
+
+        # Get only the elements that are within the FOV
+        # Mask the elem coords and the max and min elem coords for processing
+        elem_coord_min = elem_coord_min[crop_mask,:]
+        elem_coord_max = elem_coord_max[crop_mask,:]
+        num_elems_in_image = elem_coord_min.shape[0]
+
+        # Find the indices of the bounding box that each element lies within on
+        # the image, bounded by the upper and lower edges of the image
+        elem_bound_boxes_inds = np.zeros([num_elems_in_image,4],dtype=np.int32)
+        elem_bound_boxes_inds[:,0] = RasterNP.elem_bound_box_low(
+                                            elem_coord_min[:,0])
+        elem_bound_boxes_inds[:,1] = RasterNP.elem_bound_box_high(
+                                            elem_coord_max[:,0],
+                                            cam_data.pixels_count[0]-1)
+        elem_bound_boxes_inds[:,2] = RasterNP.elem_bound_box_low(
+                                            elem_coord_min[:,1])
+        elem_bound_boxes_inds[:,3] = RasterNP.elem_bound_box_high(
+                                            elem_coord_max[:,1],
+                                            cam_data.pixels_count[1]-1)
+
+        num_edges: int = 3
+        if elem_coords.shape[1] > 3:
+            num_edges = 4
+
+        mask_subpixel_buffer =  np.full(subsample*cam_data.pixels_count,0.0).T
+        # Raster Loop
+        for ee in range(elem_coords.shape[0]):
+            # Create the subpixel coords inside the bounding box to test with the
+            # edge function. Use the pixel indices of the bounding box.
+            bound_subpx_x = np.arange(elem_bound_boxes_inds[ee,0],
+                                      elem_bound_boxes_inds[ee,1],
+                                      1/subsample) + 1/(2*subsample)
+            bound_subpx_y = np.arange(elem_bound_boxes_inds[ee,2],
+                                      elem_bound_boxes_inds[ee,3],
+                                      1/subsample) + 1/(2*subsample)
+            (bound_subpx_grid_x,bound_subpx_grid_y) = np.meshgrid(bound_subpx_x,
+                                                                  bound_subpx_y)
+            bound_coords_grid_shape = bound_subpx_grid_x.shape
+            # shape=(coord[x,y],num_subpx_in_box)
+            bound_subpx_coords_flat = np.vstack((bound_subpx_grid_x.flatten(),
+                                                 bound_subpx_grid_y.flatten()))
+
+            # Create the subpixel indices for buffer slicing later
+            subpx_inds_x = np.arange(subsample*elem_bound_boxes_inds[ee,0],
+                                     subsample*elem_bound_boxes_inds[ee,1])
+            subpx_inds_y = np.arange(subsample*elem_bound_boxes_inds[ee,2],
+                                     subsample*elem_bound_boxes_inds[ee,3])
+            (subpx_inds_grid_x,subpx_inds_grid_y) = np.meshgrid(subpx_inds_x,
+                                                                subpx_inds_y)
+
+            edge = np.zeros((num_edges,bound_subpx_coords_flat.shape[1]),dtype=np.float64)
+
+            if num_edges == 4:
+                edge[0,:] = edge_function(elem_coords[ee,1,:],
+                                          elem_coords[ee,2,:],
+                                          bound_subpx_coords_flat)
+                edge[1,:] = edge_function(elem_coords[ee,2,:],
+                                          elem_coords[ee,3,:],
+                                          bound_subpx_coords_flat)
+                edge[2,:] = edge_function(elem_coords[ee,3,:],
+                                          elem_coords[ee,0,:],
+                                          bound_subpx_coords_flat)
+                edge[3,:] = edge_function(elem_coords[ee,0,:],
+                                          elem_coords[ee,1,:],
+                                          bound_subpx_coords_flat)
+            else:
+                edge[0,:] = edge_function(elem_coords[ee,1,:],
+                                          elem_coords[ee,2,:],
+                                          bound_subpx_coords_flat)
+                edge[1,:] = edge_function(elem_coords[ee,2,:],
+                                          elem_coords[ee,0,:],
+                                          bound_subpx_coords_flat)
+                edge[2,:] = edge_function(elem_coords[ee,0,:],
+                                          elem_coords[ee,1,:],
+                                          bound_subpx_coords_flat)
+
+
+            # Now we check where the edge function is above zero for all edges
+            edge_check = np.zeros_like(edge,dtype=np.int8)
+            edge_check[edge >= 0.0] = 1
+            edge_check = np.sum(edge_check, axis=0)
+            # Create a mask with the check, TODO check the 3 here for non triangles
+            edge_mask_flat = edge_check == num_edges
+            edge_mask_grid = np.reshape(edge_mask_flat,bound_coords_grid_shape)
+
+            subpx_inds_grid_x = subpx_inds_grid_x[edge_mask_grid]
+            subpx_inds_grid_y = subpx_inds_grid_y[edge_mask_grid]
+            mask_subpixel_buffer[subpx_inds_grid_y,subpx_inds_grid_x] += 1.0
+
+        mask_subpixel_buffer[mask_subpixel_buffer>1.0] = 1.0
+
+        mask_buffer = CameraTools.average_subpixel_image(mask_subpixel_buffer,
+                                                         subsample)
+        image[mask_buffer<1.0] = cam_data.background
+        return (image,mask_subpixel_buffer)
+
+
+    @staticmethod
+    def upsample_image(cam_data: CameraData2D,
+                       input_im: np.ndarray):
+        # Get grid of pixel centroid locations
+        (px_vec_xm,px_vec_ym) = CameraTools.pixel_vec_leng(cam_data.field_of_view,
+                                                           cam_data.leng_per_px)
+
+        # Get grid of sub-pixel centroid locations
+        (subpx_vec_xm,subpx_vec_ym) = CameraTools.subpixel_vec_leng(
+                                                        cam_data.field_of_view,
+                                                        cam_data.leng_per_px,
+                                                        cam_data.subsample)
+
+        # NOTE: See Scipy transition from interp2d docs here:
+        # https://scipy.github.io/devdocs/tutorial/interpolate/interp_transition_guide.html
+        spline_interp = RectBivariateSpline(px_vec_xm,
+                                            px_vec_ym,
+                                            input_im.T)
+        upsampled_image_interp = lambda x_new, y_new: spline_interp(x_new, y_new).T
+
+        # This function will flip the image regardless of the y vector input so flip it
+        # back to FE coords
+        upsampled_image =  upsampled_image_interp(subpx_vec_xm,subpx_vec_ym)
+
+        return upsampled_image
+
+
+    @staticmethod
+    def preprocess(cam_data: CameraData2D,
+                   image_input: np.ndarray,
+                   coords: np.ndarray,
+                   connectivity: np.ndarray,
+                   disp_x: np.ndarray,
+                   disp_y: np.ndarray,
+                   id_opts: ImageDefOpts,
+                   print_on: bool = False
+                   ) -> tuple[np.ndarray | None,
+                              np.ndarray | None,
+                              np.ndarray | None,
+                              np.ndarray | None,
+                              np.ndarray | None]:
+
+        if print_on:
+            print("\n"+"="*80)
+            print("IMAGE DEF PRE-PROCESSING\n")
+
+        if not id_opts.save_path.is_dir():
+            id_opts.save_path.mkdir()
+
+        # Make displacements a 2D column vector, allows addition of static frame
+        if disp_x.ndim == 1:
+            disp_x = np.atleast_2d(disp_x).T
+        if disp_y.ndim == 1:
+            disp_y = np.atleast_2d(disp_y).T
+
+        if id_opts.add_static_ref:
+            num_nodes = coords.shape[0] # type: ignore
+            disp_x = np.hstack((np.zeros((num_nodes,1)),disp_x))
+            disp_y = np.hstack((np.zeros((num_nodes,1)),disp_y))
+
+        image_input = CameraTools.crop_image_rectangle(image_input,
+                                                       cam_data.pixels_count)
+
+        if id_opts.mask_input_image or id_opts.def_complex_geom:
+            if print_on:
+                print('Image masking or complex geometry on, getting image mask.')
+                tic = time.perf_counter()
+
+            (image_input,
+             image_mask) = ImageDef2D.image_mask_from_sim(cam_data,
+                                                          image_input,
+                                                          coords,
+                                                          connectivity)
+
+
+            if print_on:
+                toc = time.perf_counter()
+                print(f'Calculating image mask took {toc-tic:.4f} seconds')
+        else:
+            image_mask = None
+
+
+        # Image upsampling
+        if print_on:
+            print('\n'+'-'*80)
+            print('GENERATE UPSAMPLED IMAGE\n')
+            print(f'Upsampling input image with a {cam_data.subsample}x{cam_data.subsample} subpixel')
+            tic = time.perf_counter()
+
+        upsampled_image = ImageDef2D.upsample_image(cam_data,image_input)
+
+        if print_on:
+            toc = time.perf_counter()
+            print(f'Upsampling image withtook {toc-tic:.4f} seconds')
+
+        return (upsampled_image,image_mask,image_input,disp_x,disp_y)
+
+    @staticmethod
+    def deform_one_image(upsampled_image: np.ndarray,
+                         cam_data: CameraData2D,
+                         id_opts: ImageDefOpts,
+                         coords: np.ndarray,
+                         disp: np.ndarray,
+                         image_mask: np.ndarray | None = None,
+                         print_on: bool = True
+                         ) -> tuple[np.ndarray,
+                                    np.ndarray,
+                                    np.ndarray,
+                                    np.ndarray,
+                                    np.ndarray | None]:
+
+        if image_mask is not None:
+            if (image_mask.shape[0] != cam_data.pixels_count[1]) or (image_mask.shape[1] != cam_data.pixels_count[0]):
+                if image_mask.size == 0:
+                    warnings.warn('Image mask not specified, using default mask of whole image.')
+                else:
+                    warnings.warn('Image mask size does not match camera, using default mask of whole image.')
+                image_mask = np.ones([cam_data.pixels_count[1],cam_data.pixels_count[0]])
+
+        (px_grid_xm,
+         px_grid_ym) = CameraTools.pixel_grid_leng(cam_data.field_of_view,
+                                                   cam_data.leng_per_px)
+
+        (subpx_grid_xm,
+         subpx_grid_ym) = CameraTools.subpixel_grid_leng(cam_data.field_of_view,
+                                                        cam_data.leng_per_px,
+                                                        cam_data.subsample)
+
+        #--------------------------------------------------------------------------
+        # Interpolate FE displacements onto the sub-pixel grid
+        if print_on:
+            print('Interpolating displacement onto sub-pixel grid.')
+            tic = time.perf_counter()
+
+        (subpx_disp_x,subpx_disp_y) = _interp_sim_disp_to_subpx_grid(
+                                                                coords,
+                                                                disp,
+                                                                cam_data,
+                                                                id_opts,
+                                                                subpx_grid_xm,
+                                                                subpx_grid_ym)
+
+        if print_on:
+            toc = time.perf_counter()
+            print('Interpolating displacement with NaN extrap took {:.4f} seconds'.format(toc-tic))
+
+        #--------------------------------------------------------------------------
+        # Interpolate sub-pixel gray levels with ndimage toolbox
+        if print_on:
+            print('Deforming sub-pixel image.')
+            tic = time.perf_counter()
+
+        def_image_subpx = _interp_subpx_image(upsampled_image,
+                                              subpx_grid_xm-subpx_disp_x,
+                                              subpx_grid_ym-subpx_disp_y,
+                                              cam_data,
+                                              id_opts)
+
+        if print_on:
+            toc = time.perf_counter()
+            print('Deforming sub-pixel image with ndimage took {:.4f} seconds'.format(toc-tic))
+
+        #--------------------------------------------------------------------------
+        # Average subpixel image
+        if print_on:
+            tic = time.perf_counter()
+
+        def_image = CameraTools.average_subpixel_image(def_image_subpx,
+                                                       cam_data.subsample)
+
+        if print_on:
+            toc = time.perf_counter()
+            print('Averaging sub-pixel imagetook {:.4f} seconds'.format(toc-tic))
+
+        #--------------------------------------------------------------------------
+        # DEFORMING IMAGE MASK
+        if id_opts.def_complex_geom:
+            if print_on:
+                print('Deforming image mask.')
+                tic = time.perf_counter()
+
+            (def_image,def_mask) = _deform_image_mask(def_image,
+                                                      image_mask,
+                                                      px_grid_xm,
+                                                      px_grid_ym,
+                                                      subpx_disp_x,
+                                                      subpx_disp_y,
+                                                      cam_data)
+
+            if print_on:
+                toc = time.perf_counter()
+                print('Deforming image mask with ndimage took {:.4f} seconds'.format(toc-tic))
+
+        else:
+            def_mask = None
+
+        # Need to flip the image as all processing above is done with y axis down
+        # from the top left hand corner
+        def_image = def_image[::-1,:]
+
+        return (def_image,def_image_subpx,subpx_disp_x,subpx_disp_y,def_mask)
+
+    @staticmethod
+    def deform_images_to_disk(cam_data: CameraData2D,
+                      upsampled_image: np.ndarray,
+                      coords: np.ndarray,
+                      connectivity: np.ndarray,
+                      disp_x: np.ndarray,
+                      disp_y: np.ndarray,
+                      image_mask: np.ndarray | None,
+                      id_opts: ImageDefOpts,
+                      print_on: bool = False) -> None:
+
+        #---------------------------------------------------------------------------
+        # Image Deformation Loop
+        if print_on:
+            print('\n'+'='*80)
+            print('DEFORMING IMAGES')
+
+        num_frames = disp_x.shape[1]
+        ticl = time.perf_counter()
+
+        for ff in range(num_frames):
+            if print_on:
+                ticf = time.perf_counter()
+                print(f'\nDEFORMING FRAME: {ff}')
+
+            disp = np.array((disp_x[:,ff],disp_y[:,ff])).T
+            (def_image,
+            _,
+            _,
+            _,
+            _) = ImageDef2D.deform_one_image(upsampled_image,
+                                            cam_data,
+                                            id_opts,
+                                            coords,
+                                            disp,
+                                            image_mask,
+                                            print_on=print_on)
+
+            save_file = id_opts.save_path / str(f'{id_opts.save_tag}_'+
+                    f'{CameraTools.image_num_str(im_num=ff,width=4)}'+
+                    '.tiff')
+            CameraTools.save_image(save_file,def_image,cam_data.bits)
+
+            if print_on:
+                tocf = time.perf_counter()
+                print(f'DEFORMING FRAME: {ff} took {tocf-ticf:.4f} seconds')
+
+        if print_on:
+            tocl = time.perf_counter()
+            print('\n'+'-'*50)
+            print(f'Deforming all images took {tocl-ticl:.4f} seconds')
+            print('-'*50)
+
+            print('\n'+'='*80)
+            print('COMPLETE\n')
+
+
+
+def _interp_sim_disp_to_subpx_grid(coords: np.ndarray,
+                               disp: np.ndarray,
+                               cam_data: CameraData2D,
+                               id_opts: ImageDefOpts,
+                               subpx_grid_xm: np.ndarray,
+                               subpx_grid_ym: np.ndarray
+                               ) -> tuple[np.ndarray,np.ndarray]:
+
+    # Interpolate displacements onto sub-pixel locations - nan extrapolation
+    subpx_disp_x = griddata((coords[:,0] + disp[:,0] + cam_data.world_to_cam[0],
+                            coords[:,1] + disp[:,1] + cam_data.world_to_cam[1]),
+                            disp[:,0],
+                            (subpx_grid_xm,subpx_grid_ym),
+                            method=id_opts.fe_interp,
+                            fill_value=np.nan,
+                            rescale=id_opts.fe_rescale)
+
+    subpx_disp_y = griddata((coords[:,0] + disp[:,0] + cam_data.world_to_cam[0],
+                            coords[:,1] + disp[:,1] + cam_data.world_to_cam[1]),
+                            disp[:,1],
+                            (subpx_grid_xm,subpx_grid_ym),
+                            method=id_opts.fe_interp,
+                            fill_value=np.nan,
+                            rescale=id_opts.fe_rescale)
+
+    # Ndimage interp can't handle nans so force everything outside the specimen
+    # to extrapolate outside the FOV - then use ndimage opts to control
+    if id_opts.fe_extrap_outside_fov:
+        subpx_disp_ext_vals = 2*cam_data.field_of_view
+    else:
+        subpx_disp_ext_vals = (0.0,0.0)
+
+    # Set the nans to the extrapoltion value
+    subpx_disp_x[np.isnan(subpx_disp_x)] = subpx_disp_ext_vals[0]
+    subpx_disp_y[np.isnan(subpx_disp_y)] = subpx_disp_ext_vals[1]
+
+    return (subpx_disp_x,subpx_disp_y)
+
+
+def _interp_subpx_image(upsampled_image: np.ndarray,
+                        def_subpx_x: np.ndarray,
+                        def_subpx_y: np.ndarray,
+                        cam_data: CameraData2D,
+                        id_opts: ImageDefOpts,
+                        ) -> np.ndarray:
+
+        # Flip needed to be consistent with pixel coords of ndimage
+        def_subpx_x = def_subpx_x[::-1,:]
+        def_subpx_y = def_subpx_y[::-1,:]
+
+        # NDIMAGE: IMAGE DEF
+        # NOTE: need to shift to pixel centroid co-ords from nodal so -0.5 makes the
+        # top left 0,0 in pixel co-ords
+        def_subpx_x_in_px = def_subpx_x*(cam_data.subsample/cam_data.leng_per_px)-0.5
+        def_subpx_y_in_px = def_subpx_y*(cam_data.subsample/cam_data.leng_per_px)-0.5
+        # NOTE: prefilter needs to be on to match griddata and interp2D!
+        # with prefilter on this exactly matches I2D but 10x faster!
+        def_image_subpx = ndimage.map_coordinates(upsampled_image,
+                                                [[def_subpx_y_in_px],
+                                                [def_subpx_x_in_px]],
+                                                prefilter=True,
+                                                order= id_opts.image_def_order,
+                                                mode= id_opts.image_def_extrap,
+                                                cval= id_opts.image_def_extval)
+
+        def_image_subpx = def_image_subpx[0,:,:].squeeze()
+
+        return def_image_subpx
+
+
+def _deform_image_mask(def_image: np.ndarray,
+                       image_mask: np.ndarray,
+                       px_grid_xm: np.ndarray,
+                       px_grid_ym: np.ndarray,
+                       subpx_disp_x: np.ndarray,
+                       subpx_disp_y: np.ndarray,
+                       cam_data: CameraData2D,
+                       ) -> tuple[np.ndarray,np.ndarray]:
+
+    # This is slow - might be quicker to just deform an upsampled mask
+    px_disp_x = CameraTools.average_subpixel_image(subpx_disp_x,
+                                                   cam_data.subsample)
+    px_disp_y = CameraTools.average_subpixel_image(subpx_disp_y,
+                                                   cam_data.subsample)
+
+    def_px_x = px_grid_xm-px_disp_x
+    def_px_y = px_grid_ym-px_disp_y
+    # Flip needed to be consistent with pixel coords of ndimage
+    def_px_x = def_px_x[::-1,:]
+    def_px_y = def_px_y[::-1,:]
+
+    # NDIMAGE: DEFORM IMAGE MASK
+    # NOTE: need to shift to pixel centroid co-ords from nodal so -0.5 makes the
+    # top left 0,0 in pixel co-ords
+    def_px_x_in_px = def_px_x*(1/cam_data.leng_per_px)-0.5
+    def_px_y_in_px = def_px_y*(1/cam_data.leng_per_px)-0.5
+    # NOTE: prefilter needs to be on to match griddata and interp2D!
+    # with prefilter on this exactly matches I2D but 10x faster!
+    def_mask = ndimage.map_coordinates(image_mask,
+                                        [[def_px_y_in_px],
+                                        [def_px_x_in_px]],
+                                        prefilter=True,
+                                        order=2,
+                                        mode='constant',
+                                        cval=0)
+
+    def_mask = def_mask[0,:,:].squeeze()
+    # Use the deformed image mask to mask the deformed image
+    # Mask is 0-1 with 1 being definitely inside the sample 0 outside
+    def_image[def_mask<0.51] = cam_data.background # type: ignore
+
+    return (def_image,image_mask)