From ca065a5ed7260feb03fd2edbd1275ab87c033748 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 30 Aug 2024 12:05:03 +0200 Subject: [PATCH] Reflecting update of nxdefs --- src/pynxtools_em/methods/ebsd.py | 8 +++--- src/pynxtools_em/methods/eds.py | 45 ++++---------------------------- 2 files changed, 10 insertions(+), 43 deletions(-) diff --git a/src/pynxtools_em/methods/ebsd.py b/src/pynxtools_em/methods/ebsd.py index 06e7b9b..9456890 100644 --- a/src/pynxtools_em/methods/ebsd.py +++ b/src/pynxtools_em/methods/ebsd.py @@ -308,7 +308,7 @@ def ebsd_roi_overview(inp: EbsdPointCloud, id_mgn: dict, template: dict) -> dict if not trg_grid.descr_type: return template - trg = f"/ENTRY[entry{id_mgn['entry_id']}]/ROI[roi{id_mgn['roi_id']}]/ebsd/indexing/roi" + trg = f"/ENTRY[entry{id_mgn['entry_id']}]/roiID[roi{id_mgn['roi_id']}]/ebsd/indexing/roi" template[f"{trg}/descriptor"] = trg_grid.descr_type template[f"{trg}/title"] = ( f"Region-of-interest overview image ({trg_grid.descr_type})" @@ -365,7 +365,9 @@ def ebsd_roi_overview(inp: EbsdPointCloud, id_mgn: dict, template: dict) -> dict def ebsd_roi_phase_ipf(inp: EbsdPointCloud, id_mgn: dict, template: dict) -> dict: """Create for each phase three inverse pole figures (IPF) maps projected along X, Y using for each map only the respective scan points that were indexed for this phase.""" nxem_phase_id = 0 - prfx = f"/ENTRY[entry{id_mgn['entry_id']}]/ROI[roi{id_mgn['roi_id']}]/ebsd/indexing" + prfx = ( + f"/ENTRY[entry{id_mgn['entry_id']}]/roiID[roi{id_mgn['roi_id']}]/ebsd/indexing" + ) # bookkeeping for how many scan points solutions were found is always for src_grid # because the eventual discretization for h5web is solely # for the purpose of showing users a readily consumable default plot @@ -479,7 +481,7 @@ def process_roi_phase_ipf( # 2D, 0 > y, 1 > x # 1D, 0 > x trg = ( - f"/ENTRY[entry{id_mgn['entry_id']}]/ROI[roi{id_mgn['roi_id']}]/ebsd/indexing" + f"/ENTRY[entry{id_mgn['entry_id']}]/roiID[roi{id_mgn['roi_id']}]/ebsd/indexing" f"/phaseID[phase{nxem_phase_id}]/ipfID[ipf{idx + 1}]" ) template[f"{trg}/projection_direction"] = np.asarray( diff --git a/src/pynxtools_em/methods/eds.py b/src/pynxtools_em/methods/eds.py index 4b0a501..95eed4b 100644 --- a/src/pynxtools_em/methods/eds.py +++ b/src/pynxtools_em/methods/eds.py @@ -20,45 +20,10 @@ import numpy as np from pynxtools_em.concepts.nxs_image_set import NxImageRealSpaceSet -# process_roi_eds_spectra(inp, template) -# process_roi_eds_maps(inp, template) -# if ckey.startswith("eds_roi") and inp[ckey] != {}: -# self.process_roi_overview_eds_based(inp[ckey], template) +# TODO::all functions here are work in progress -def process_roi_overview_eds_based(self, inp, template: dict) -> dict: - trg = ( - f"/ENTRY[entry{self.entry_id}]/measurement/event_data_em_set/" - f"EVENT_DATA_EM[event_data_em{self.id_mgn['event']}]/" - f"IMAGE_SET[image_set{self.id_mgn['event_img']}]/image_2d" - ) - template[f"{trg}/description"] = inp.tmp["source"] - template[f"{trg}/title"] = f"Region-of-interest overview image" - template[f"{trg}/@signal"] = "real" - dims = [("i", 0), ("j", 1)] - template[f"{trg}/@axes"] = [] - for dim in dims[::-1]: - template[f"{trg}/@axes"].append(f"axis_{dim[0]}") - template[f"{trg}/real"] = { - "compress": inp.tmp["image_2d/real"].value, - "strength": 1, - } - template[f"{trg}/real/@long_name"] = f"Signal" - for dim in dims: - template[f"{trg}/@AXISNAME_indices[axis_{dim[0]}_indices]"] = np.uint32(dim[1]) - template[f"{trg}/AXISNAME[axis_{dim[0]}]"] = { - "compress": inp.tmp[f"image_2d/axis_{dim[0]}"].value, - "strength": 1, - } - template[f"{trg}/AXISNAME[axis_{dim[0]}]/@long_name"] = inp.tmp[ - f"image_2d/axis_{dim[0]}@long_name" - ].value - self.id_mgn["event_img"] += 1 - self.id_mgn["event"] += 1 - return template - - -def process_roi_eds_spectra(self, inp: dict, template: dict) -> dict: +def eds_roi_summary(self, inp: dict, template: dict) -> dict: for ckey in inp.keys(): if ckey.startswith("eds_spc") and inp[ckey] != {}: trg = ( @@ -90,11 +55,11 @@ def process_roi_eds_spectra(self, inp: dict, template: dict) -> dict: return template -def process_roi_eds_maps(self, inp: dict, template: dict) -> dict: +def eds_roi_eds_map(self, inp: dict, template: dict) -> dict: for ckey in inp.keys(): if ckey.startswith("eds_map") and inp[ckey] != {}: trg = ( - f"/ENTRY[entry{self.entry_id}]/ROI[roi{self.id_mgn['roi']}]/" + f"/ENTRY[entry{self.entry_id}]/roiID[roi{self.id_mgn['roi']}]/" f"eds/indexing" ) template[f"{trg}/source"] = inp[ckey].tmp["source"] @@ -102,7 +67,7 @@ def process_roi_eds_maps(self, inp: dict, template: dict) -> dict: if not isinstance(img, NxImageRealSpaceSet): continue trg = ( - f"/ENTRY[entry{self.entry_id}]/ROI[roi{self.id_mgn['roi']}]/eds/" + f"/ENTRY[entry{self.entry_id}]/roiID[roi{self.id_mgn['roi']}]/eds/" f"indexing/IMAGE_SET[image_set{self.id_mgn['eds_img']}]" ) template[f"{trg}/source"] = img.tmp["source"]