Merge pull request #217 from jonwright/master

Point by point scanner for sinograms
FABLE-3DXRD · Feb 12, 2024 · 54d6461 · 54d6461
2 parents a8f80bb + f937175
commit 54d6461
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diff --git a/ImageD11/nbGui/run_pbp.ipynb b/ImageD11/nbGui/run_pbp.ipynb
@@ -0,0 +1,192 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import sys, os\n",
+    "os.environ['OMP_NUM_THREADS']='1'\n",
+    "sys.path.insert(0, f'{os.environ[\"HOME\"]}/git/ImageD11')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import ImageD11.sinograms.point_by_point\n",
+    "import ImageD11.sinograms.dataset\n",
+    "import ImageD11.sinograms.properties\n",
+    "from ImageD11.blobcorrector import eiger_spatial\n",
+    "import ImageD11.columnfile\n",
+    "import pylab as pl, numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!pwd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "parname = '/data/visitor/ihma423/id11/20231205/PROCESSED_DATA/S7_deformed/Al_fcc_2.par'\n",
+    "SparsePixelFolder = '/data/visitor/ihma423/id11/20231205/PROCESSED_DATA/SparsePixels_NewMask/'\n",
+    "sample = 'S9_355C_10min_3rd'\n",
+    "dset_prefix = 'sliceZ_-360um'\n",
+    "cf_postfix = '4rha'\n",
+    "\n",
+    "z = 5\n",
+    "if 1:\n",
+    "    \n",
+    "    dsname = os.path.join(SparsePixelFolder, 'ds_' + sample + '_' + dset_prefix + '_' + str(z) + '.h5')\n",
+    "    pksname = os.path.join(SparsePixelFolder, 'pks_' + sample + '_' + dset_prefix + '_' + str(z) + '.h5')\n",
+    "    outname = os.path.join(SparsePixelFolder, sample + '_' + dset_prefix + '_' + str(z) + '_sparse.h5')                  \n",
+    "    cf_h5 = os.path.join(os.getcwd(), sample + '_' + dset_prefix + '_' + str(z) + '_' + cf_postfix + '.h5')               \n",
+    "    pbp_out = os.path.join(os.getcwd(), sample + '_' + dset_prefix + '_' + str(z) + '_' + cf_postfix + '.pbp')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "pk = ImageD11.sinograms.properties.pks_table.load(pksname)\n",
+    "dset = ImageD11.sinograms.dataset.load(dsname)\n",
+    "es = eiger_spatial(dxfile='/data/id11/nanoscope/Eiger/e2dx_E-08-0173_20231127.edf',\n",
+    "                   dyfile='/data/id11/nanoscope/Eiger/e2dy_E-08-0173_20231127.edf' )\n",
+    "cf = ImageD11.columnfile.colfile_from_dict( es(pk.pk2d(dset.omega, dset.dty)) )\n",
+    "cf.filter(cf.Number_of_pixels > 5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "p= ImageD11.sinograms.point_by_point.PBP(\n",
+    "    parname,\n",
+    "    dset,\n",
+    "    hkl_tol=0.01,\n",
+    "        fpks=0.7,\n",
+    "        ds_tol=0.01,\n",
+    "        etacut=0.1,\n",
+    "        ifrac=1./300,\n",
+    "        cosine_tol=np.cos(np.radians(90 - 0.1)),\n",
+    "        y0=0,\n",
+    "        symmetry=\"cubic\",\n",
+    "        foridx=[0, 1, 2, 4, 5],\n",
+    "        forgen=[5, 1],\n",
+    "        uniqcut=0.75)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "p.setpeaks(cf)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "f, ax = p.iplot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "p.point_by_point('grainsout2.pbp', nprocs=1, debugpoints=[(10,10),], loglevel=0)\n",
+    "!tail grainsout2.pbp"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "p.point_by_point('grainsout_all.pbp', loglevel=3)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (main)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}