Merge branch 'FABLE-3DXRD:master' into master

Author: jonwright

ImageD11/forward_model/forward_projector.py

@@ -4,7 +4,8 @@
 # Suitable for both s3DXRD using pencil beam and box-beam 3DXRD
 # Haixing Fang, haixing.fang@esrf.fr
 # Jan 2nd, 2025
-# updated on January 30, 2025
+# version 1.0: updated on January 30, 2025
+# version 1.1: fixed a bug with ray origin on December 10, 2025
 
 import numpy as np
 from matplotlib import pyplot as plt
@@ -726,7 +727,7 @@ def read_cf(self):
                     self.cf_4d = colfile_from_hdf(self.cf_4d_file)
                     self.peaks_4d = io.convert_cf_to_fwd_peaks(self.cf_4d)
                     if self.verbose >= 1:
-                        logging.info('loaded 4D peaks from {}'.format(self.cf_4d_file))   
+                        logging.info('loaded 4D peaks from {}'.format(self.cf_4d_file))
         else:
             self.get_cf()
 
@@ -973,11 +974,17 @@ def intersected_sample_pos(mask, dty = 0.0, y0_offset = 0.0, voxel_size = [1.0,
 
     if not isinstance(voxel_size, np.ndarray):
         voxel_size = np.array(voxel_size, dtype='float')
+    #Omega = forward_model.get_omega_matrix(np.deg2rad(-omega))
+    #ray_direction = np.dot(Omega, [1.0, 0.0, 0.0])
+    #grid_size = mask.shape
+    #assert len(grid_size) == 3, "The input mask must be in 3D"
+    #ray_origin = [0.0, -dty - y0_offset, 0.0]
+    
     Omega = forward_model.get_omega_matrix(np.deg2rad(-omega))
     ray_direction = np.dot(Omega, [1.0, 0.0, 0.0])
     grid_size = mask.shape
     assert len(grid_size) == 3, "The input mask must be in 3D"
-    ray_origin = [0.0, -dty - y0_offset, 0.0]
+    ray_origin = np.dot(Omega, [0.0, -dty - y0_offset, 0.0]) # the absolute distance between the ray and the rotation center keeps as a constant of dty+y0_offset
 
     intersected_voxels = intersected_voxels_3d(grid_size, ray_origin, ray_direction, voxel_size = voxel_size,
                                                ray_size=ray_size, weight = weight, weight_pos = weight_pos, mask = mask, plot_flag = plot_flag)
@@ -1028,8 +1035,12 @@ def intersected_voxels_3d(grid_size, ray_origin, ray_direction, voxel_size = [1.
     grid_extent = np.array(grid_size) * voxel_size
     max_extent = np.linalg.norm(grid_extent)
 
-    t_values = np.linspace(-0.707 * max_extent + ray_origin[1], 0.707 * max_extent + ray_origin[1], int(max(grid_size)*1.414))
-    ray_shift = np.array([grid_size[1] / 2 + 0.5, grid_size[1] / 2 + 0.5, 0.0]) * voxel_size
+    #t_values = np.linspace(-0.707 * max_extent + ray_origin[1], 0.707 * max_extent + ray_origin[1], int(max(grid_size)*1.414))
+    #ray_shift = np.array([grid_size[1] / 2 + 0.5, grid_size[1] / 2 + 0.5, 0.0]) * voxel_size
+    #ray_path = np.array(ray_origin) / voxel_size + ray_shift + np.outer(t_values, ray_direction)
+
+    t_values = np.linspace(-0.707 * max_extent + np.linalg.norm(ray_origin), 0.707 * max_extent + np.linalg.norm(ray_origin), int(max(grid_size)*1.414))
+    ray_shift = np.array([grid_size[0] / 2 + 0.5, grid_size[1] / 2 + 0.5, 0.0]) * voxel_size
     ray_path = np.array(ray_origin) / voxel_size + ray_shift + np.outer(t_values, ray_direction)
 
     tol_distances = np.array(weight_pos)*ray_size
@@ -1348,11 +1359,11 @@ def ensure_2d_array(target_hkls):
 
 def plot_fwd_peaks(fwd_peaks):
     assert fwd_peaks.shape[1] == 25, "fwd_peaks shapes are not qualified"
-    f, ax = plt.subplots(1, 2, figsize=(15, 9))
+    f, ax = plt.subplots(1, 2, figsize=(12, 6))
 
     sc = ax[0].scatter(fwd_peaks[:, 18], fwd_peaks[:, 19], c=fwd_peaks[:, 23], cmap='viridis', s=8)
     ax[0].set_aspect('equal', 'box')
-    cb = f.colorbar(sc, ax=ax[0])
+    cb = f.colorbar(sc, ax=ax[0], fraction=0.046, pad=0.04)
     # cb.set_label('Intensity', fontsize = 20)
     cb.ax.tick_params(labelsize=14)
     ax[0].set_xlabel('fc (pixel)', fontsize = 20)
@@ -1363,7 +1374,7 @@ def plot_fwd_peaks(fwd_peaks):
 
     sc = ax[1].scatter(fwd_peaks[:, 5], fwd_peaks[:, 6], c=fwd_peaks[:, 23], cmap='viridis', s=8)
     ax[1].set_aspect('equal', 'box')
-    cb = f.colorbar(sc, ax=ax[1])
+    cb = f.colorbar(sc, ax=ax[1], fraction=0.046, pad=0.04)
     cb.set_label('Intensity', fontsize = 20)
     cb.ax.tick_params(labelsize=14)
     ax[1].set_xlabel('X (mm)', fontsize = 20)

ImageD11/forward_model/grainmaps.py

@@ -94,21 +94,27 @@ def convert2DS(self):
         convert tensor_map to a dictionary like DS, which is similar to fwd-DCT struct, easier for subsequent operation
         """
         tensor_map = self.read_tensor_map()
-        
+        tensor_map_flag = False
         for key in tensor_map.keys():
             if 'TensorMap' in key:
                 print('Got the key name {}'.format(key))
                 keyname = key
+                tensor_map_flag = True
 
         print('********************* Converting to DS format *****************************')
         keys_list = ['B', 'U', 'UB', 'UBI', 'eps_sample', 'euler', 'ipf_x', 'ipf_y', 'ipf_z', 'mt', 'nuniq', 'phase_ids', 'unitcell', 'intensity', 'labels']
-        DS = {}
-        for k in keys_list:
-            if k in tensor_map[keyname]['maps'].keys():
-                print('Loading {} with a shape of {} to DS ...'.format(k, tensor_map[keyname]['maps'][k].shape))
-                DS[k] = tensor_map[keyname]['maps'][k]
-        if 'step' in tensor_map[keyname].keys():
-            DS['voxel_size'] = tensor_map[keyname]['step'] # [um/pixel]
+        if tensor_map_flag:
+            # it reads directly as a tensor map
+            DS = {}
+            for k in keys_list:
+                if k in tensor_map[keyname]['maps'].keys():
+                    print('Loading {} with a shape of {} to DS ...'.format(k, tensor_map[keyname]['maps'][k].shape))
+                    DS[k] = tensor_map[keyname]['maps'][k]
+            if 'step' in tensor_map[keyname].keys():
+                DS['voxel_size'] = tensor_map[keyname]['step'] # [um/pixel]
+        else:
+            # the provided map is a DS-like dictionary map already
+            DS = tensor_map
 
 
         DS['Rod'] = np.empty((DS['UBI'].shape[0], DS['UBI'].shape[1], DS['UBI'].shape[2], 3))

ImageD11/forward_model/test_forward_projector_to_cf.ipynb

@@ -8,7 +8,8 @@
     "# Test forward_projector.py\n",
     "## Test to generate peaks forward computed from an experimentally reconstructed grain map and convert peaks to cf\n",
     "## Haixing Fang\n",
-    "## Jan 2025"
+    "## Created in Jan 2025\n",
+    "## Updated in Dec 2025"
    ]
   },
   {
@@ -160,7 +161,9 @@
    },
    "outputs": [],
    "source": [
-    "fp = forward_projector.forward_projector(sample_filename, pars_filename, phase_name, detector_mask = None, to_sparse = False, **opts)"
+    "# specify the output_folder according to your needs\n",
+    "fp = forward_projector.forward_projector(sample_filename, pars_filename, phase_name, detector_mask = None,\n",
+    "                                         to_sparse = False, output_folder = None, **opts)"
    ]
   },
   {
@@ -457,24 +460,25 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "704fba35-e632-4a7d-8b0e-39999bd26070",
-   "metadata": {
-    "tags": []
-   },
+   "id": "8a11ccca-482b-4fb6-bb00-67d2e093674f",
+   "metadata": {},
    "outputs": [],
    "source": [
-    "Al = ImageD11.unitcell.unitcell_from_parameters(pars)"
+    "# load phases from parameter file\n",
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cff1f3c5-b279-4bcb-880d-8f5eb04fd120",
-   "metadata": {
-    "tags": []
-   },
+   "id": "7c412300-017b-42d8-9602-8a513d4877a5",
+   "metadata": {},
    "outputs": [],
    "source": [
+    "phase_str = 'Al'\n",
+    "Al = ds.phases.unitcells[phase_str]\n",
+    "print(Al)\n",
     "Al.makerings(1.5)"
    ]
   },
@@ -828,7 +832,14 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.9"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,