Merge pull request #345 from jadball/master

Fix strain to stress conversion in TensorMap class, better TensorMap documentation
FABLE-3DXRD · Nov 6, 2024 · d039e0c · d039e0c
2 parents 927ca86 + f159837
commit d039e0c
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Showing 16 changed files with 624 additions and 604 deletions.
diff --git a/ImageD11/nbGui/S3DXRD/4_visualise.ipynb b/ImageD11/nbGui/S3DXRD/4_visualise.ipynb
@@ -92,7 +92,8 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "ds.phases = ds.get_phases_from_disk()"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/5_combine_phases.ipynb b/ImageD11/nbGui/S3DXRD/5_combine_phases.ipynb
@@ -86,8 +86,7 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "phases = ds.get_phases_from_disk()\n",
-    "ds.phases = phases\n",
+    "ds.phases = ds.get_phases_from_disk()\n",
     "ds.phases.unitcells"
    ]
   },

diff --git a/ImageD11/nbGui/S3DXRD/6_stack_layers.ipynb b/ImageD11/nbGui/S3DXRD/6_stack_layers.ipynb
@@ -83,6 +83,19 @@
     "print(ds.shape)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8ea038db-b86c-4ce3-9117-83060f68351e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# load phases from parameter file\n",
+    "\n",
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -95,12 +108,12 @@
     "samples_dict = {}\n",
     "\n",
     "skips_dict = {\n",
-    "    \"FeAu_0p5_tR_nscope\": [\"top_100um\", \"top_-100um\"]\n",
+    "    ds.sample: []\n",
     "}\n",
     "\n",
     "dset_prefix = \"top\"\n",
     "\n",
-    "sample_list = [\"FeAu_0p5_tR_nscope\"]\n",
+    "sample_list = [ds.sample]\n",
     "\n",
     "for sample in sample_list:\n",
     "    all_dset_folders_for_sample = os.listdir(os.path.join(rawdata_path, sample))\n",
@@ -114,8 +127,7 @@
     "    samples_dict[sample] = dsets_list\n",
     "    \n",
     "# manually override:\n",
-    "\n",
-    "samples_dict = {\"FeAu_0p5_tR_nscope\": [\"top_150um\", \"top_200um\", \"top_250um\"]}"
+    "# samples_dict = {\"FeAu_0p5_tR_nscope\": [\"top_150um\", \"top_200um\", \"top_250um\"]}"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/pbp_2_visualise.ipynb b/ImageD11/nbGui/S3DXRD/pbp_2_visualise.ipynb
@@ -88,7 +88,8 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "ds.phases = ds.get_phases_from_disk()"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb b/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb
@@ -100,7 +100,8 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "ds.phases = ds.get_phases_from_disk()"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/tomo_1_index.ipynb b/ImageD11/nbGui/S3DXRD/tomo_1_index.ipynb
@@ -260,10 +260,10 @@
     "\n",
     "fig, ax = plt.subplots(figsize=(16, 9), constrained_layout=True)\n",
     "\n",
-    "ax.plot( ucell.ringds, [1e4,]*len(ucell.ringds), '|', ms=90, c=\"red\")\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",

diff --git a/ImageD11/nbGui/S3DXRD/tomo_1_index_minor_phase.ipynb b/ImageD11/nbGui/S3DXRD/tomo_1_index_minor_phase.ipynb
diff --git a/ImageD11/nbGui/TDXRD/0_3DXRD_segment_frelon.ipynb b/ImageD11/nbGui/TDXRD/0_3DXRD_segment_frelon.ipynb
@@ -366,27 +366,39 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ac6a298f-1405-4d90-b677-7a29c04de67e",
+   "id": "53e92fd0-8088-4746-b2bb-2735a7cd015e",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Now that weparfile happy with our indexing parameters, we can run the below cell to do this in bulk for many samples/datasets\n",
+    "# Now that we are happy with our segmentation parameters, we can run the below cell to do this in bulk for many samples/datasets\n",
     "# by default this will do all samples in sample_list, all datasets with a prefix of dset_prefix\n",
     "# you can add samples and datasets to skip in skips_dict\n",
     "\n",
     "skips_dict = {\n",
     "    \"FeAu_0p5_tR\": []\n",
     "}\n",
     "\n",
+    "# USER: Change this prefix to match the naming convention of your datasets\n",
+    "# e.g if your slices are formatted like [\"ff_z0\", \"ff_z1\", \"ff_z2\"] etc, then the prefix could be \"ff\" or \"ff_z\"\n",
+    "\n",
     "dset_prefix = \"ff\"\n",
     "\n",
     "sample_list = [\"FeAu_0p5_tR\"]\n",
     "    \n",
     "samples_dict = utils.find_datasets_to_process(ds.dataroot, skips_dict, dset_prefix, sample_list)\n",
-    "    \n",
-    "# manual override:\n",
-    "# samples_dict = {\"FeAu_0p5_tR\": [\"ff1\", \"ff2\"]}\n",
+    "print(samples_dict)\n",
     "\n",
+    "# manual override example:\n",
+    "# samples_dict = {\"FeAu_0p5_tR\": [\"ff1\", \"ff2\"]}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ac6a298f-1405-4d90-b677-7a29c04de67e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "for sample, datasets in samples_dict.items():\n",
     "    for dataset in datasets:\n",
     "        print(f\"Processing dataset {dataset} in sample {sample}\")\n",

diff --git a/ImageD11/nbGui/TDXRD/1_3DXRD_refine_parameters.ipynb b/ImageD11/nbGui/TDXRD/1_3DXRD_refine_parameters.ipynb
@@ -72,8 +72,10 @@
    "outputs": [],
    "source": [
     "# desination of H5 files\n",
+    "# replace below with e.g.:\n",
+    "# dset_path = '/data/visitor/expt1234/20240101/PROCESSED_DATA/sample/dataset/sample_dataset.h5'\n",
     "\n",
-    "dset_path = '/data/visitor/ihma439/id11/20231211/PROCESSED_DATA/James/20240909/FeAu_0p5_tR/FeAu_0p5_tR_ff1/FeAu_0p5_tR_ff1_dataset.h5'"
+    "dset_path = ''"
    ]
   },
   {
@@ -94,6 +96,16 @@
     "print(ds.shape)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -102,9 +114,6 @@
    },
    "outputs": [],
    "source": [
-    "ds.phases = ds.get_phases_from_disk()\n",
-    "ds.phases.unitcells\n",
-    "\n",
     "# now let's select a phase to index from our parameters json\n",
     "phase_str = 'Fe'\n",
     "\n",
@@ -203,10 +212,11 @@
     "\n",
     "fig, ax = plt.subplots(figsize=(16, 9), constrained_layout=True)\n",
     "\n",
-    "ax.plot( ucell.ringds, [1e4,]*len(ucell.ringds), '|', ms=90, c=\"red\")\n",
+    "\n",
     "\n",
     "ax.plot(cf_3d.ds, cf_3d.sum_intensity,',', label='cf_3d')\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",
     "ax.semilogy()\n",
     "\n",
     "ax.set_xlabel(\"Dstar\")\n",

diff --git a/ImageD11/nbGui/TDXRD/2_3DXRD_index.ipynb b/ImageD11/nbGui/TDXRD/2_3DXRD_index.ipynb
@@ -68,8 +68,10 @@
    "outputs": [],
    "source": [
     "# desination of H5 files\n",
+    "# replace below with e.g.:\n",
+    "# dset_path = '/data/visitor/expt1234/20240101/PROCESSED_DATA/sample/dataset/sample_dataset.h5'\n",
     "\n",
-    "dset_path = '/data/visitor/ihma439/id11/20231211/PROCESSED_DATA/James/20240909/FeAu_0p5_tR/FeAu_0p5_tR_ff1/FeAu_0p5_tR_ff1_dataset.h5'"
+    "dset_path = ''"
    ]
   },
   {
@@ -90,6 +92,16 @@
     "print(ds.shape)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -98,9 +110,6 @@
    },
    "outputs": [],
    "source": [
-    "ds.phases = ds.get_phases_from_disk()\n",
-    "ds.phases.unitcells\n",
-    "\n",
     "# now let's select a phase to index from our parameters json\n",
     "phase_str = 'Fe'\n",
     "\n",
@@ -208,10 +217,10 @@
     "\n",
     "fig, ax = plt.subplots(figsize=(16, 9), constrained_layout=True)\n",
     "\n",
-    "ax.plot(ucell.ringds, [1e4,]*len(ucell.ringds), '|', ms=90, c=\"red\")\n",
-    "\n",
     "ax.plot(cf_3d.ds, cf_3d.sum_intensity,',', label='cf_3d')\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",
@@ -639,7 +648,7 @@
     "    unindexed_flt_path,\n",
     "    map_path,\n",
     "    final_unindexed_flt_path,\n",
-    "    final_new_flt_path\n",
+    "    final_new_flt_path,\n",
     "]:\n",
     "    if os.path.exists(path):\n",
     "        os.remove(path)"
@@ -662,23 +671,34 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Now that we're happy with our indexing parameters, we can run the below cell to do this in bulk for many samples/datasets\n",
+    "# Now that we are happy with our indexing parameters, we can run the below cell to do this in bulk for many samples/datasets\n",
     "# by default this will do all samples in sample_list, all datasets with a prefix of dset_prefix\n",
     "# you can add samples and datasets to skip in skips_dict\n",
     "\n",
     "skips_dict = {\n",
     "    \"FeAu_0p5_tR\": []\n",
     "}\n",
     "\n",
+    "# USER: Change this prefix to match the naming convention of your datasets\n",
+    "# e.g if your slices are formatted like [\"ff_z0\", \"ff_z1\", \"ff_z2\"] etc, then the prefix could be \"ff\" or \"ff_z\"\n",
+    "\n",
     "dset_prefix = \"ff\"\n",
     "\n",
     "sample_list = [\"FeAu_0p5_tR\"]\n",
+    "    \n",
+    "samples_dict = utils.find_datasets_to_process(ds.dataroot, skips_dict, dset_prefix, sample_list)\n",
+    "print(samples_dict)\n",
     "\n",
-    "rawdata_path = ds.dataroot\n",
-    "processed_data_root_dir = ds.analysisroot\n",
-    "samples_dict = utils.find_datasets_to_process(rawdata_path, skips_dict, dset_prefix, sample_list)\n",
-    "\n",
-    "\n",
+    "# manual override example:\n",
+    "# samples_dict = {\"FeAu_0p5_tR\": [\"ff1\", \"ff2\"]}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "for sample, datasets in samples_dict.items():\n",
     "    for dataset in datasets:\n",
     "        print(f\"Processing dataset {dataset} in sample {sample}\")\n",
@@ -783,7 +803,7 @@
     "            unindexed_flt_path,\n",
     "            map_path,\n",
     "            final_unindexed_flt_path,\n",
-    "            final_new_flt_path\n",
+    "            final_new_flt_path,\n",
     "        ]:\n",
     "            if os.path.exists(path):\n",
     "                os.remove(path)\n",