3D EBSD working

FAIRmat-NFDI · Nov 9, 2023 · 33688c1 · 33688c1
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commit 33688c1
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Showing 4 changed files with 15 additions and 11 deletions.
diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_dreamthreed.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_dreamthreed.py
@@ -379,7 +379,7 @@ def parse_and_normalize_ebsd_data(self, ckey: str):
                 h5r[f"{self.path_registry['group_data']}/Phases"], np.int32)
             old_shp = np.shape(self.tmp[ckey]["phase_id"])
             self.tmp[ckey]["phase_id"] = np.reshape(self.tmp[ckey]["phase_id"],
-                                                    (int(np.prod(old_shp[0:3])), int(old_shp[3])),
+                                                    (int(np.prod(old_shp[0:3])),),
                                                     order="C")
             print(np.unique(self.tmp[ckey]["phase_id"]))
             # Phases here stores C-style index which Phase of the possible ones

diff --git a/pynxtools/dataconverter/readers/em/subparsers/nxs_hfive.py b/pynxtools/dataconverter/readers/em/subparsers/nxs_hfive.py
@@ -562,7 +562,8 @@ def onthefly_process_roi_ipfs_phases_threed(self, inp: dict, roi_id: int, templa
         template[f"{prfx}/indexing_rate"] = np.float64(100. * n_pts_indexed / n_pts)
         template[f"{prfx}/indexing_rate/@units"] = f"%"
         grp_name = f"{prfx}/EM_EBSD_CRYSTAL_STRUCTURE_MODEL[phase{phase_id}]"
-        template[f"{grp_name}/number_of_scan_points"] = np.uint32(0)
+        template[f"{grp_name}/number_of_scan_points"] \
+            = np.uint32(np.sum(inp["phase_id"] == 0))
         template[f"{grp_name}/phase_identifier"] = np.uint32(phase_id)
         template[f"{grp_name}/phase_name"] = f"notIndexed"
 
@@ -611,7 +612,7 @@ def process_roi_phase_ipfs_threed(self,
                 direction=PROJECTION_VECTORS[idx])
             img = get_ipfdir_legend(ipf_key)
 
-            rotations = Rotation.from_euler(euler=inp["euler"][inp["phases"] == pyxem_phase_id],
+            rotations = Rotation.from_euler(euler=inp["euler"][inp["phase_id"] == pyxem_phase_id],
                                             direction='lab2crystal',
                                             degrees=False)
             print(f"shape rotations -----> {np.shape(rotations)}")
@@ -625,7 +626,7 @@ def process_roi_phase_ipfs_threed(self,
             # but IPF color maps have a whitepoint which encodes in fact an orientation
             # and because of that we may have a single crystal with an orientation
             # close to the whitepoint which become a fully white seemingly "empty" image
-            ipf_rgb_map[inp["phases"] == pyxem_phase_id, :] = rgb_px_with_phase_id
+            ipf_rgb_map[inp["phase_id"] == pyxem_phase_id, :] = rgb_px_with_phase_id
             ipf_rgb_map = np.reshape(
                 ipf_rgb_map, (inp["n_z"], inp["n_y"], inp["n_x"], 3), order="C")
             # 0 is z, 1 is y, while 2 is x !
@@ -653,16 +654,17 @@ def process_roi_phase_ipfs_threed(self,
             template[f"{mpp}/DATA[data]"] = {"compress": ipf_rgb_map, "strength": 1}
             hfive_web_decorate_nxdata(f"{mpp}/DATA[data]", template)
 
-            scan_unit = inp["s_unit"]  # this is not correct necessarily as the
-            # simulation may be scale-invariant...
+            scan_unit = inp["s_unit"]  # TODO::this is not necessarily correct
+            # could be a scale-invariant synthetic microstructure whose simulation
+            # would work on multiple length-scales as atoms are not resolved directly!
             if scan_unit == "um":
                 scan_unit = "µm"
             for dim in dims:
                 template[f"{mpp}/AXISNAME[axis_{dim}]"] \
-                = {"compress": self.get_named_axis(inp, f"{dim}"), "strength": 1}
-            template[f"{mpp}/AXISNAME[axis_{dim}]/@long_name"] \
-                = f"Coordinate along {dim}-axis ({scan_unit})"
-            template[f"{mpp}/AXISNAME[axis_{dim}]/@units"] = f"{scan_unit}"
+                    = {"compress": self.get_named_axis(inp, f"{dim}"), "strength": 1}
+                template[f"{mpp}/AXISNAME[axis_{dim}]/@long_name"] \
+                    = f"Coordinate along {dim}-axis ({scan_unit})"
+                template[f"{mpp}/AXISNAME[axis_{dim}]/@units"] = f"{scan_unit}"
 
             # add the IPF color map legend/key
             lgd = f"{trg}/DATA[legend]"
@@ -672,6 +674,7 @@ def process_roi_phase_ipfs_threed(self,
             template[f"{lgd}/@NX_class"] = f"NXdata"  # TODO::writer should decorate automatically!
             template[f"{lgd}/@signal"] = "data"
             template[f"{lgd}/@axes"] = []
+            dims = ["x", "y"]
             for dim in dims[::-1]:
                 template[f"{lgd}/@axes"].append(f"axis_{dim}")
             enum = 0

diff --git a/pynxtools/dataconverter/readers/em/utils/hfive_web_constants.py b/pynxtools/dataconverter/readers/em/utils/hfive_web_constants.py
@@ -28,4 +28,5 @@ def hfive_web_decorate_nxdata(path: str, inp: dict) -> dict:
         inp[f"{path}/@CLASS"] = f"IMAGE"  # required by H5Web to plot RGB maps
         inp[f"{path}/@IMAGE_VERSION"] = f"1.2"
         inp[f"{path}/@SUBCLASS_VERSION"] = np.int64(15)
+        inp[f"{path}/@long_name"] = f"Signal"
     return inp
diff --git a/test.ebsd3d_hdf5.sh b/test.ebsd3d_hdf5.sh
@@ -17,7 +17,7 @@ Examples="067_0003 SmallIN100_Final 244_0014"
 
 
 # Examples="SmallIN100_Final"
-Examples="244_0014"
+# Examples="244_0014"
 for example in $Examples; do
 	echo $example
 	dataconverter --reader em --nxdl NXroot --input-file $example.dream3d --output debug.$example.dream3d.nxs 1>stdout.$example.dream3d.nxs.txt 2>stderr.$example.dream3d.nxs.txt