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Merge pull request #276 from jadball/master
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Geometry overhaul (+tests), update all notebooks
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@jonwright
jonwright authored Apr 11, 2024
2 parents 62ae918 + c1b9dbb commit a1b1e1b
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22 changes: 7 additions & 15 deletions ImageD11/nbGui/3DXRD/0_3DXRD_segment_frelon.ipynb
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Expand Up @@ -126,6 +126,8 @@
"\n",
"from frelon_peaksearch import worker, process\n",
"\n",
"from ImageD11.blobcorrector import correct_cf_with_spline\n",
"\n",
"# from utils import apply_spatial"
]
},
Expand Down Expand Up @@ -162,17 +164,7 @@
"\n",
"### USER: specify where you want your processed data to go\n",
"\n",
"processed_data_root_dir = \"/data/visitor/ihma439/id11/20231211/PROCESSED_DATA/James/nb_testing\"# NOTE: For old datasets before the new directory layout structure, we don't distinguish between RAW_DATA and PROCESSED_DATA\n",
"\n",
"### USER: specify your experimental directory\n",
"\n",
"rawdata_path = \"/data/visitor/ihma439/id11/20231211/RAW_DATA\"\n",
"\n",
"!ls -lrt {rawdata_path}\n",
"\n",
"### USER: specify where you want your processed data to go\n",
"\n",
"processed_data_root_dir = \"/data/visitor/ihma439/id11/20231211/PROCESSED_DATA/James/nb_testing\""
"processed_data_root_dir = \"/data/visitor/ihma439/id11/20231211/PROCESSED_DATA/James/nb_testing\"# NOTE: For old datasets before the new directory layout structure, we don't distinguish between RAW_DATA and PROCESSED_DATA"
]
},
{
Expand Down Expand Up @@ -429,7 +421,7 @@
},
"outputs": [],
"source": [
"cf_2d = utils.apply_spatial_lut(cf_2d, spline_file)"
"cf_2d = correct_cf_with_spline(cf_2d, spline_file)"
]
},
{
Expand All @@ -441,7 +433,7 @@
},
"outputs": [],
"source": [
"cf_3d = utils.apply_spatial_lut(cf_3d, spline_file)"
"cf_3d = correct_cf_with_spline(cf_3d, spline_file)"
]
},
{
Expand Down Expand Up @@ -566,8 +558,8 @@
" cf_2d, cf_3d = process(ds, nthreads-1, worker_args)\n",
" \n",
" print(\"Spatially correcting peaks\")\n",
" cf_2d = utils.apply_spatial_lut(cf_2d, spline_file)\n",
" cf_3d = utils.apply_spatial_lut(cf_3d, spline_file)\n",
" cf_2d = correct_cf_with_spline(cf_2d, spline_file)\n",
" cf_3d = correct_cf_with_spline(cf_3d, spline_file)\n",
" \n",
" print(\"Saving peaks to file\")\n",
" cf_2d.parameters.loadparameters(parfile)\n",
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102 changes: 43 additions & 59 deletions ImageD11/nbGui/3DXRD/2_3DXRD_index.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,8 @@
"import ImageD11.columnfile\n",
"from ImageD11.sinograms import properties, dataset\n",
"\n",
"from ImageD11.blobcorrector import eiger_spatial"
"from ImageD11.blobcorrector import eiger_spatial\n",
"from ImageD11.peakselect import select_ring_peaks_by_intensity"
]
},
{
Expand Down Expand Up @@ -144,13 +145,10 @@
"source": [
"# load 3d columnfile from disk\n",
"\n",
"cf_3d = ImageD11.columnfile.colfile_from_hdf(ds.col3dfile)\n",
"cf_3d = ds.get_cf_3d_from_disk()\n",
"\n",
"cf_3d.parameters.loadparameters(ds.parfile)\n",
"cf_3d.updateGeometry()\n",
"\n",
"if \"index\" not in cf_3d.titles:\n",
" cf_3d.addcolumn(np.arange(cf_3d.nrows), \"index\")"
"cf_3d.updateGeometry()"
]
},
{
Expand Down Expand Up @@ -194,7 +192,7 @@
"cf_strong_dsmax = 1.03\n",
"cf_strong_dstol = 0.01\n",
"\n",
"cf_strong = utils.selectpeaks(cf_3d, frac=cf_strong_frac, dsmax=cf_strong_dsmax, doplot=0.8, dstol=cf_strong_dstol)\n",
"cf_strong = select_ring_peaks_by_intensity(cf_3d, frac=cf_strong_frac, dsmax=cf_strong_dsmax, doplot=0.8, dstol=cf_strong_dstol)\n",
"print(f\"Got {cf_strong.nrows} strong peaks for indexing\")\n",
"cf_strong.writefile(f'{sample}_{dataset}_3d_peaks_strong.flt')"
]
Expand All @@ -213,7 +211,7 @@
"cf_strong_allrings_frac = 0.95\n",
"cf_strong_allrings_dstol = 0.01\n",
"\n",
"cf_strong_allrings = utils.selectpeaks(cf_3d, frac=cf_strong_allrings_frac, dsmax=cf_3d.ds.max(), doplot=0.8, dstol=cf_strong_allrings_dstol)\n",
"cf_strong_allrings = select_ring_peaks_by_intensity(cf_3d, frac=cf_strong_allrings_frac, dsmax=cf_3d.ds.max(), doplot=0.8, dstol=cf_strong_allrings_dstol)\n",
"print(f\"Got {cf_strong_allrings.nrows} strong peaks for makemap\")\n",
"cf_strong_allrings_path = f'{sample}_{dataset}_3d_peaks_strong_all_rings.flt'\n",
"cf_strong_allrings.writefile(cf_strong_allrings_path)"
Expand Down Expand Up @@ -361,13 +359,34 @@
" g.gid = i"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# let's look at the pole figures\n",
"# for this we need to set a reference unit cell for the grains\n",
"\n",
"cf_pars = cf_strong.parameters.get_parameters()\n",
"spacegroup = 229 # spacegroup for BCC iron\n",
"cf_pars[\"cell_lattice_[P,A,B,C,I,F,R]\"] = spacegroup\n",
"\n",
"ref_ucell = ImageD11.unitcell.unitcell_from_parameters(cf_pars)\n",
"\n",
"for g in grains:\n",
" g.ref_unitcell = ref_ucell"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# plot pole figures?"
"utils.plot_all_ipfs(grains)"
]
},
{
Expand Down Expand Up @@ -507,7 +526,7 @@
"outputs": [],
"source": [
"# find the spike\n",
"absolute_minpks = 45"
"absolute_minpks = 37"
]
},
{
Expand Down Expand Up @@ -563,36 +582,11 @@
},
"outputs": [],
"source": [
"for grain in grains_filtered:\n",
" grain.gid = int(grain.name.split(\":\")[0])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# now we will assign all our 3D peaks to our grains"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"peak_assignment_hkl_tol = 0.05\n",
"# now we will assign all our 3D peaks to our remaining grains\n",
"\n",
"utils.assign_peaks_to_grains(grains_filtered, cf_3d, tol)\n",
"peak_assignment_hkl_tol = 0.05\n",
"\n",
"print(\"Storing peak data in grains\")\n",
"# iterate through all the grains\n",
"for g in tqdm(grains_filtered):\n",
" # store this grain's peak indices so we know which 3D peaks we used for indexing\n",
" g.peaks_3d = cf_3d.index[cf_3d.grain_id == g.gid]"
"utils.assign_peaks_to_grains(grains_filtered, cf_3d, peak_assignment_hkl_tol)"
]
},
{
Expand All @@ -603,11 +597,9 @@
},
"outputs": [],
"source": [
"fig, ax = plt.subplots()\n",
"ax.hist([np.mean(grain.unitcell[0:3]) for grain in grains_filtered], bins=25)\n",
"plt.show()\n",
"# re-save our now indexed peaks\n",
"\n",
"print(np.mean([np.mean(grain.unitcell[0:3]) for grain in grains_filtered]))"
"ImageD11.columnfile.colfile_to_hdf(cf_3d, ds.col3dfile, name=\"peaks\")"
]
},
{
Expand All @@ -620,7 +612,7 @@
"source": [
"# save grain data\n",
"\n",
"utils.save_3dxrd_grains(grains_filtered, ds)"
"ds.save_grains_to_disk(grains_filtered)"
]
},
{
Expand Down Expand Up @@ -691,21 +683,18 @@
" print(f\"Found existing grains file for {dataset} in {sample}, skipping\")\n",
" continue\n",
"\n",
"\n",
" print(\"Loading 3D peaks\")\n",
" cf_3d = ImageD11.columnfile.colfile_from_hdf(ds.col3dfile)\n",
" cf_3d = ds.get_cf_3d_from_disk()\n",
" cf_3d.parameters.loadparameters(ds.parfile)\n",
" cf_3d.updateGeometry()\n",
" if \"index\" not in cf_3d.titles:\n",
" cf_3d.addcolumn(np.arange(cf_3d.nrows), \"index\")\n",
"\n",
" print(\"Filtering 3D peaks\")\n",
" cf_strong = utils.selectpeaks(cf_3d, frac=cf_strong_frac, dsmax=cf_strong_dsmax, doplot=None, dstol=cf_strong_dstol)\n",
" cf_strong = select_ring_peaks_by_intensity(cf_3d, frac=cf_strong_frac, dsmax=cf_strong_dsmax, doplot=None, dstol=cf_strong_dstol)\n",
" print(f\"Got {cf_strong.nrows} strong peaks for indexing\")\n",
" cf_strong_path = f'{sample}_{dataset}_3d_peaks_strong.flt'\n",
" cf_strong.writefile(cf_strong_path)\n",
"\n",
" cf_strong_allrings = utils.selectpeaks(cf_3d, frac=cf_strong_allrings_frac, dsmax=cf_3d.ds.max(), doplot=None, dstol=cf_strong_allrings_dstol)\n",
" cf_strong_allrings = select_ring_peaks_by_intensity(cf_3d, frac=cf_strong_allrings_frac, dsmax=cf_3d.ds.max(), doplot=None, dstol=cf_strong_allrings_dstol)\n",
" print(f\"Got {cf_strong_allrings.nrows} strong peaks for makemap\")\n",
" cf_strong_allrings_path = f'{sample}_{dataset}_3d_peaks_strong_all_rings.flt'\n",
" cf_strong_allrings.writefile(cf_strong_allrings_path)\n",
Expand Down Expand Up @@ -752,19 +741,12 @@
" \n",
" grains_filtered = [grain for grain in grains2 if float(grain.npks) > absolute_minpks]\n",
"\n",
" for grain in grains_filtered:\n",
" grain.gid = int(grain.name.split(\":\")[0])\n",
"\n",
" utils.assign_peaks_to_grains(grains_filtered, cf_3d, tol=peak_assignment_hkl_tol)\n",
"\n",
" print(\"Storing peak data in grains\")\n",
" # iterate through all the grains\n",
" for g in tqdm(grains_filtered):\n",
" # store this grain's peak indices so we know which 3D peaks we used for indexing\n",
" g.peaks_3d = cf_3d.index[cf_3d.grain_id == g.gid]\n",
" ImageD11.columnfile.colfile_to_hdf(cf_3d, ds.col3dfile, name=\"peaks\")\n",
"\n",
" print(\"Saving grains\")\n",
" utils.save_3dxrd_grains(grains_filtered, ds)\n",
" ds.save_grains_to_disk(grains_filtered)\n",
"\n",
" if os.path.exists(cf_strong_path):\n",
" os.remove(cf_strong_path)\n",
Expand All @@ -782,7 +764,9 @@
" os.remove(new_flt_path)\n",
"\n",
" if os.path.exists(unindexed_flt_path):\n",
" os.remove(unindexed_flt_path)"
" os.remove(unindexed_flt_path)\n",
"\n",
"print(\"Done!\")"
]
},
{
Expand Down
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