Merge pull request #349 from jadball/master

Various notebook quality-of-life changes, some TensorMap stuff
FABLE-3DXRD · Nov 12, 2024 · 8db3d8d · 8db3d8d
2 parents 83ad4d7 + 36ebde2
commit 8db3d8d
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Showing 11 changed files with 313 additions and 243 deletions.
diff --git a/ImageD11/frelon_peaksearch.py b/ImageD11/frelon_peaksearch.py
@@ -372,6 +372,8 @@ def process(ds, worker_args, ncpu=None):
     """
     if ncpu is None:
         nthreads = max(1, ImageD11.cImageD11.cores_available() - 1)
+    else:
+        nthreads = int(ncpu)
     hname = ds.masterfile
     scan_name = ds.scans[0]
     frames_dset = scan_name + "/measurement/" + ds.detector

diff --git a/ImageD11/nbGui/S3DXRD/pbp_1_indexing.ipynb b/ImageD11/nbGui/S3DXRD/pbp_1_indexing.ipynb
@@ -32,6 +32,12 @@
    },
    "outputs": [],
    "source": [
+    "import os\n",
+    "\n",
+    "os.environ['OMP_NUM_THREADS'] = '1'\n",
+    "os.environ['OPENBLAS_NUM_THREADS'] = '1'\n",
+    "os.environ['MKL_NUM_THREADS'] = '1'\n",
+    "\n",
     "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
     "PYTHONPATH = setup_ImageD11_from_git( ) # ( os.path.join( os.environ['HOME'],'Code'), 'ImageD11_git' )"
    ]

diff --git a/ImageD11/nbGui/S3DXRD/run_astra_recon.py b/ImageD11/nbGui/S3DXRD/run_astra_recon.py
@@ -1,16 +1,23 @@
 def main(h5name, dsfile, group_name):
+    print('Loading dataset')
     # load the dataset
     ds = ImageD11.sinograms.dataset.load(dsfile)
-
+
+    print('Loading grain sinograms from disk')
     grainsinos = read_h5(h5name, ds, group_name=group_name)
-
-    for gs in grainsinos:
+
+    print('Reconstructing grain sinograms')
+    for inc, gs in enumerate(grainsinos):
         gs.recon(method="astra", astra_method="EM_CUDA")
+        print('Reconstructed ' + inc+1 + '/' + len(grainsinos))
 
     # mask recon after running
+    print('Masking reconstructions')
     for gs in grainsinos:
         gs.recons['astra'] = np.where(gs.recon_mask, gs.recons['astra'], 0)
-
+
+    print('Reconstructions finished')
+    print('Writing grains to disk')
     write_h5(h5name, grainsinos, overwrite_grains=True, group_name=group_name)
 
 

diff --git a/ImageD11/nbGui/S3DXRD/tomo_1_index.ipynb b/ImageD11/nbGui/S3DXRD/tomo_1_index.ipynb
@@ -186,7 +186,7 @@
     "\n",
     "ucell.makerings(cf_4d.ds.max())\n",
     "\n",
-    "fig, ax = plt.subplots(figsize=(16,9), layout='constrained')\n",
+    "fig, ax = plt.subplots(figsize=(10,5), layout='constrained')\n",
     "\n",
     "ax.scatter(cf_4d.ds, cf_4d.eta, s=1)\n",
     "ax.plot( ucell.ringds, [0,]*len(ucell.ringds), '|', ms=90, c=\"red\")\n",
@@ -258,7 +258,7 @@
    "source": [
     "# now we can take a look at the intensities of the remaining peaks\n",
     "\n",
-    "fig, ax = plt.subplots(figsize=(16, 9), constrained_layout=True)\n",
+    "fig, ax = plt.subplots(figsize=(10, 5), constrained_layout=True)\n",
     "\n",
     "ax.plot(cf_4d.ds, cf_4d.sum_intensity,',', label='cf_4d')\n",
     "ax.plot(cf_strong.ds, cf_strong.sum_intensity,',', label='cf_strong')\n",
@@ -324,7 +324,7 @@
    "source": [
     "# let's plot the assigned peaks\n",
     "\n",
-    "fig, ax = plt.subplots(layout='constrained', figsize=(16,9))\n",
+    "fig, ax = plt.subplots(layout='constrained', figsize=(10,5))\n",
     "\n",
     "# indexer.ra is the ring assignments\n",
     "\n",
@@ -360,7 +360,7 @@
     "# the sequence of minpks fractions the indexer will iterate through\n",
     "fracs = [0.9, 0.7]\n",
     "# the tolerance in g-vector angle\n",
-    "cosine_tol = np.cos(np.radians(90 - 0.25))\n",
+    "cosine_tol = np.cos(np.radians(90 - ds.ostep))\n",
     "# the max number of UBIs we can find per pair of rings\n",
     "max_grains = 1000\n",
     "\n",
@@ -447,7 +447,7 @@
    },
    "outputs": [],
    "source": [
-    "utils.plot_grain_sinograms(grains, cf_strong)"
+    "utils.plot_grain_sinograms(grains, cf_strong, min(len(grains), 25))"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/tomo_2_map.ipynb b/ImageD11/nbGui/S3DXRD/tomo_2_map.ipynb
@@ -26,6 +26,12 @@
    },
    "outputs": [],
    "source": [
+    "import os\n",
+    "\n",
+    "os.environ['OMP_NUM_THREADS'] = '1'\n",
+    "os.environ['OPENBLAS_NUM_THREADS'] = '1'\n",
+    "os.environ['MKL_NUM_THREADS'] = '1'\n",
+    "\n",
     "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
     "PYTHONPATH = setup_ImageD11_from_git( ) # ( os.path.join( os.environ['HOME'],'Code'), 'ImageD11_git' )"
    ]
@@ -110,7 +116,9 @@
    "outputs": [],
    "source": [
     "# pick a phase\n",
-    "phase_str = 'Fe'"
+    "phase_str = 'Fe'\n",
+    "\n",
+    "ucell = ds.phases.unitcells[phase_str]"
    ]
   },
   {
@@ -178,6 +186,29 @@
     "cf_strong.nrows"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# now we can take a look at the intensities of the remaining peaks\n",
+    "\n",
+    "fig, ax = plt.subplots(figsize=(10, 5), constrained_layout=True)\n",
+    "\n",
+    "ax.plot(cf_4d.ds, cf_4d.sum_intensity,',', label='cf_4d')\n",
+    "ax.plot(cf_strong.ds, cf_strong.sum_intensity,',', label='cf_strong')\n",
+    "ax.plot(ucell.ringds, [1e4,]*len(ucell.ringds), '|', ms=90, c=\"red\")\n",
+    "\n",
+    "ax.semilogy()\n",
+    "\n",
+    "ax.set_xlabel(\"Dstar\")\n",
+    "ax.set_ylabel(\"Intensity\")\n",
+    "ax.legend()\n",
+    "\n",
+    "plt.show()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/ImageD11/nbGui/S3DXRD/tomo_2_map_minor_phase.ipynb b/ImageD11/nbGui/S3DXRD/tomo_2_map_minor_phase.ipynb
@@ -27,6 +27,12 @@
    },
    "outputs": [],
    "source": [
+    "import os\n",
+    "\n",
+    "os.environ['OMP_NUM_THREADS'] = '1'\n",
+    "os.environ['OPENBLAS_NUM_THREADS'] = '1'\n",
+    "os.environ['MKL_NUM_THREADS'] = '1'\n",
+    "\n",
     "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
     "PYTHONPATH = setup_ImageD11_from_git( ) # ( os.path.join( os.environ['HOME'],'Code'), 'ImageD11_git' )"
    ]

diff --git a/ImageD11/nbGui/TDXRD/2_3DXRD_index.ipynb b/ImageD11/nbGui/TDXRD/2_3DXRD_index.ipynb
@@ -306,7 +306,7 @@
     "# the sequence of minpks fractions the indexer will iterate through\n",
     "fracs = [0.9, 0.75]\n",
     "# the tolerance in g-vector angle\n",
-    "cosine_tol = np.cos(np.radians(90 - 0.25))\n",
+    "cosine_tol = np.cos(np.radians(90 - ds.ostep))\n",
     "# the max number of UBIs we can find per pair of rings\n",
     "max_grains = 1000\n",
     "\n",
@@ -342,6 +342,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# inverse pole figure of grain orientations\n",
+    "\n",
     "utils.plot_all_ipfs(grains)"
    ]
   },
@@ -434,7 +436,12 @@
    "source": [
     "# re-import our refined grains from the makemap procedure\n",
     "\n",
-    "grains2 = ImageD11.grain.read_grain_file(tmp_map_path)"
+    "grains2 = ImageD11.grain.read_grain_file(tmp_map_path)\n",
+    "\n",
+    "for g in grains2:\n",
+    "    g.ref_unitcell = ucell\n",
+    "\n",
+    "utils.get_rgbs_for_grains(grains2)"
    ]
   },
   {
@@ -458,29 +465,9 @@
    },
    "outputs": [],
    "source": [
-    "centre_plot = False\n",
-    "\n",
-    "fig = plt.figure(figsize=(12, 12))\n",
-    "ax = fig.add_subplot(projection='3d')\n",
-    "xx = [grain.translation[0] for grain in grains2]\n",
-    "yy = [grain.translation[1] for grain in grains2]\n",
-    "zz = [grain.translation[2] for grain in grains2]\n",
-    "# col = [utils.grain_to_rgb(grain) for grain in grains2]  # IPF-Z colour instead\n",
-    "col = [float(grain.npks) for grain in grains2]\n",
-    "sizes = [0.01*(float(grain.intensity_info.split(\"mean = \")[1].split(\" , \")[0].replace(\"'\", \"\"))) for grain in grains2]\n",
-    "if centre_plot:\n",
-    "    scatterplot = ax.scatter(xx-np.mean(xx), yy-np.mean(yy), zz, c=col, s=sizes)\n",
-    "else:\n",
-    "    scatterplot = ax.scatter(xx, yy, zz, c=col, s=sizes)\n",
-    "ax.set_xlim(-200,200)\n",
-    "ax.set_ylim(-200,200)\n",
-    "ax.set_zlim(-200,200)\n",
-    "plt.colorbar(scatterplot)\n",
-    "ax.set_title(\"Grains coloured by n peaks\")\n",
-    "ax.set_xlabel(\"x\")\n",
-    "ax.set_ylabel(\"y\")\n",
-    "ax.set_zlabel(\"z\")\n",
-    "plt.show()"
+    "# 3D scatter plot of grain positions coloured by grain volume\n",
+    "\n",
+    "utils.plot_grain_positions(grains2, colour='npks', centre_plot=False, size_scaling=0.5)"
    ]
   },
   {
@@ -528,29 +515,9 @@
    },
    "outputs": [],
    "source": [
-    "centre_plot = False\n",
-    "\n",
-    "fig = plt.figure(figsize=(12, 12))\n",
-    "ax = fig.add_subplot(projection='3d')\n",
-    "xx = [grain.translation[0] for grain in grains_filtered]\n",
-    "yy = [grain.translation[1] for grain in grains_filtered]\n",
-    "zz = [grain.translation[2] for grain in grains_filtered]\n",
-    "# col = [utils.grain_to_rgb(grain) for grain in grains_filtered]  # IPF-Z colour instead\n",
-    "col = [float(grain.npks) for grain in grains_filtered]\n",
-    "sizes = [0.01*(float(grain.intensity_info.split(\"mean = \")[1].split(\" , \")[0].replace(\"'\", \"\"))) for grain in grains_filtered]\n",
-    "if centre_plot:\n",
-    "    scatterplot = ax.scatter(xx-np.mean(xx), yy-np.mean(yy), zz, c=col, s=sizes)\n",
-    "else:\n",
-    "    scatterplot = ax.scatter(xx, yy, zz, c=col, s=sizes)\n",
-    "ax.set_xlim(-200,200)\n",
-    "ax.set_ylim(-200,200)\n",
-    "ax.set_zlim(-200,200)\n",
-    "plt.colorbar(scatterplot)\n",
-    "ax.set_title(\"Grains coloured by n peaks\")\n",
-    "ax.set_xlabel(\"x\")\n",
-    "ax.set_ylabel(\"y\")\n",
-    "ax.set_zlabel(\"z\")\n",
-    "plt.show()"
+    "# 3D scatter plot of grain positions coloured by grain volume\n",
+    "\n",
+    "utils.plot_grain_positions(grains_filtered, colour='npks', centre_plot=False, size_scaling=0.5)"
    ]
   },
   {
@@ -584,6 +551,31 @@
     "grains_filtered = ImageD11.grain.read_grain_file(map_path)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# compute IPF colours for grains\n",
+    "\n",
+    "for g in grains_filtered:\n",
+    "    g.ref_unitcell = ucell\n",
+    "\n",
+    "utils.get_rgbs_for_grains(grains_filtered)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# inverse pole figure of grain orientations\n",
+    "\n",
+    "utils.plot_all_ipfs(grains_filtered)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -592,9 +584,20 @@
    },
    "outputs": [],
    "source": [
-    "# save grain data\n",
+    "# 3D scatter plot of grain positions coloured by grain volume\n",
     "\n",
-    "ds.save_grains_to_disk(grains_filtered, phase_name=phase_str)"
+    "utils.plot_grain_positions(grains_filtered, colour='npks', centre_plot=False, size_scaling=0.5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# 3D scatter plot of grain positions coloured by inverse pole figure orientation\n",
+    "\n",
+    "utils.plot_grain_positions(grains_filtered, colour='z', centre_plot=False, size_scaling=0.5)"
    ]
   },
   {
@@ -605,29 +608,9 @@
    },
    "outputs": [],
    "source": [
-    "centre_plot = False\n",
-    "\n",
-    "fig = plt.figure(figsize=(12, 12))\n",
-    "ax = fig.add_subplot(projection='3d')\n",
-    "xx = [grain.translation[0] for grain in grains_filtered]\n",
-    "yy = [grain.translation[1] for grain in grains_filtered]\n",
-    "zz = [grain.translation[2] for grain in grains_filtered]\n",
-    "# col = [utils.grain_to_rgb(grain) for grain in grains_filtered]  # IPF-Z colour instead\n",
-    "col = [float(grain.npks) for grain in grains_filtered]\n",
-    "sizes = [0.01*(float(grain.intensity_info.split(\"mean = \")[1].split(\" , \")[0].replace(\"'\", \"\"))) for grain in grains_filtered]\n",
-    "if centre_plot:\n",
-    "    scatterplot = ax.scatter(xx-np.mean(xx), yy-np.mean(yy), zz, c=col, s=sizes)\n",
-    "else:\n",
-    "    scatterplot = ax.scatter(xx, yy, zz, c=col, s=sizes)\n",
-    "ax.set_xlim(-200,200)\n",
-    "ax.set_ylim(-200,200)\n",
-    "ax.set_zlim(-200,200)\n",
-    "plt.colorbar(scatterplot)\n",
-    "ax.set_title(\"Grains coloured by n peaks\")\n",
-    "ax.set_xlabel(\"x\")\n",
-    "ax.set_ylabel(\"y\")\n",
-    "ax.set_zlabel(\"z\")\n",
-    "plt.show()"
+    "# save grain data\n",
+    "\n",
+    "ds.save_grains_to_disk(grains_filtered, phase_name=phase_str)"
    ]
   },
   {