Merge pull request #237 from jadball/scanbooks

Weekend feedback for scanning notebooks
FABLE-3DXRD · Mar 4, 2024 · 6662056 · 6662056
2 parents 8283041 + 2f96a3b
commit 6662056
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diff --git a/ImageD11/nbGui/3DXRD/0_3DXRD_segment_frelon.ipynb b/ImageD11/nbGui/3DXRD/0_3DXRD_segment_frelon.ipynb
@@ -40,11 +40,12 @@
    "source": [
     "import os\n",
     "\n",
-    "username = os.environ.get(\"USER\")\n",
+    "home_dir = !echo $HOME\n",
+    "home_dir = str(home_dir[0])\n",
     "\n",
     "# USER: You can change this location if you want\n",
     "\n",
-    "id11_code_path = f\"/home/esrf/{username}/Code/ImageD11\"\n",
+    "id11_code_path = os.path.join(home_dir, \"Code/ImageD11\")\n",
     "\n",
     "# check whether we already have ImageD11 here\n",
     "\n",
@@ -77,17 +78,16 @@
    },
    "outputs": [],
    "source": [
-    "# There is a bug with the current version of ImageD11 in the site-wide Jupyter env.\n",
-    "# This has been fixed here: https://github.com/FABLE-3DXRD/ImageD11/commit/4af88b886b1775585e868f2339a0eb975401468f\n",
-    "# Until a new release has been made and added to the env, we need to get the latest version of ImageD11 from GitHub\n",
-    "# Put it in your home directory\n",
     "# USER: Change the path below to point to your local copy of ImageD11:\n",
     "\n",
     "import os\n",
     "\n",
-    "username = os.environ.get(\"USER\")\n",
+    "home_dir = !echo $HOME\n",
+    "home_dir = str(home_dir[0])\n",
     "\n",
-    "id11_code_path = f\"/home/esrf/{username}/Code/ImageD11\"\n",
+    "# USER: You can change this location if you want\n",
+    "\n",
+    "id11_code_path = os.path.join(home_dir, \"Code/ImageD11\")\n",
     "\n",
     "import sys\n",
     "\n",
@@ -391,13 +391,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39fc939e-a6cd-425f-8fea-2b65e2551358",
+   "id": "88fe5554-8b0a-4c17-a2a1-02536e476c42",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "cf_2d = utils.apply_spatial(cf_2d, spline_file, nthreads)"
+    "cf_2d = utils.apply_spatial_lut(cf_2d, spline_file)"
    ]
   },
   {
@@ -409,7 +409,7 @@
    },
    "outputs": [],
    "source": [
-    "cf_3d = utils.apply_spatial(cf_3d, spline_file, nthreads)"
+    "cf_3d = utils.apply_spatial_lut(cf_3d, spline_file)"
    ]
   },
   {
@@ -472,9 +472,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Now that we're happy with our segmentation parameters, we can run the below cell to do this in bulk for many samples/datasets\n",
+    "# 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",
     "# 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\n",
+    "# you can add samples and datasets to skip in skips_dict\n",
     "\n",
     "skips_dict = {\n",
     "    \"FeAu_0p5_tR\": []\n",

diff --git a/ImageD11/nbGui/3DXRD/1_3DXRD_refine_parameters.ipynb b/ImageD11/nbGui/3DXRD/1_3DXRD_refine_parameters.ipynb
@@ -32,17 +32,16 @@
    },
    "outputs": [],
    "source": [
-    "# There is a bug with the current version of ImageD11 in the site-wide Jupyter env.\n",
-    "# This has been fixed here: https://github.com/FABLE-3DXRD/ImageD11/commit/4af88b886b1775585e868f2339a0eb975401468f\n",
-    "# Until a new release has been made and added to the env, we need to get the latest version of ImageD11 from GitHub\n",
-    "# Put it in your home directory\n",
     "# USER: Change the path below to point to your local copy of ImageD11:\n",
     "\n",
     "import os\n",
     "\n",
-    "username = os.environ.get(\"USER\")\n",
+    "home_dir = !echo $HOME\n",
+    "home_dir = str(home_dir[0])\n",
     "\n",
-    "id11_code_path = f\"/home/esrf/{username}/Code/ImageD11\"\n",
+    "# USER: You can change this location if you want\n",
+    "\n",
+    "id11_code_path = os.path.join(home_dir, \"Code/ImageD11\")\n",
     "\n",
     "import sys\n",
     "\n",
@@ -128,7 +127,7 @@
     "\n",
     "# USER: specify the path to the parameter file\n",
     "\n",
-    "parfile = '/home/esrf/james1997a/Data/ihma439/id11/20231211/PROCESSED_DATA/James/20240226/Fe_refined_tdxrd.par'\n",
+    "parfile = '/home/esrf/james1997a/Data/ihma439/id11/20231211/PROCESSED_DATA/James/20240226/Fe_tdxrd_refined.par'\n",
     "spline_file = '/data/id11/inhouse1/ewoks/detectors/files/Frelon2k_C36/frelon36.spline'"
    ]
   },
@@ -197,14 +196,14 @@
    },
    "outputs": [],
    "source": [
-    "# here we are filtering our peaks (cf_2d) to select only the strongest ones for indexing purposes only!\n",
-    "# dsmax is being set to limit rings given to the indexer\n",
-    "# because we have so many 3d peaks, we will filter down to 3 rings\n",
+    "# here we are filtering our peaks (cf_3d) to select only the strongest ones for indexing purposes only!\n",
+    "# dsmax is being set to limit rings given to the indexer - 6-8 rings is normally good\n",
     "\n",
-    "# USER: modify the \"frac\" parameter below and re-run the cell until we have around 10,000 peaks for indexing\n",
-    "# we may choose more for the full index in the next notebook, but for now we want to quickly index only our strong grains\n",
+    "# USER: modify the \"frac\" parameter below and re-run the cell until the orange dot sits nicely on the \"elbow\" of the blue line\n",
+    "# this indicates the fractional intensity cutoff we will select\n",
+    "# if the blue line does not look elbow-shaped in the logscale plot, try changing the \"doplot\" parameter (the y scale of the logscale plot) until it does\n",
     "\n",
-    "cf_strong = utils.selectpeaks(cf_3d, frac=0.95, dsmax=0.92, doplot=0.05, dstol=0.01)\n",
+    "cf_strong = utils.selectpeaks(cf_3d, frac=0.985, dsmax=0.92, doplot=0.8, dstol=0.01)\n",
     "print(f\"Got {cf_strong.nrows} strong peaks for indexing\")\n",
     "cf_strong.writefile(f'{sample}_{dataset}_3d_peaks_strong.flt')"
    ]

diff --git a/ImageD11/nbGui/3DXRD/2_3DXRD_index.ipynb b/ImageD11/nbGui/3DXRD/2_3DXRD_index.ipynb
@@ -24,17 +24,16 @@
    },
    "outputs": [],
    "source": [
-    "# There is a bug with the current version of ImageD11 in the site-wide Jupyter env.\n",
-    "# This has been fixed here: https://github.com/FABLE-3DXRD/ImageD11/commit/4af88b886b1775585e868f2339a0eb975401468f\n",
-    "# Until a new release has been made and added to the env, we need to get the latest version of ImageD11 from GitHub\n",
-    "# Put it in your home directory\n",
     "# USER: Change the path below to point to your local copy of ImageD11:\n",
     "\n",
     "import os\n",
     "\n",
-    "username = os.environ.get(\"USER\")\n",
+    "home_dir = !echo $HOME\n",
+    "home_dir = str(home_dir[0])\n",
     "\n",
-    "id11_code_path = f\"/home/esrf/{username}/Code/ImageD11\"\n",
+    "# USER: You can change this location if you want\n",
+    "\n",
+    "id11_code_path = os.path.join(home_dir, \"Code/ImageD11\")\n",
     "\n",
     "import sys\n",
     "\n",
@@ -211,13 +210,14 @@
    },
    "outputs": [],
    "source": [
-    "# here we are filtering our peaks (cf_2d) to select only the strongest ones for indexing purposes only!\n",
-    "# dsmax is being set to limit rings given to the indexer\n",
-    "# because we have so many 3d peaks, we will filter down to 3 rings\n",
+    "# here we are filtering our peaks (cf_3d) to select only the strongest ones for indexing purposes only!\n",
+    "# dsmax is being set to limit rings given to the indexer - 6-8 rings is normally good\n",
     "\n",
-    "# USER: modify the \"frac\" parameter below and re-run the cell until we have around 25,000 peaks for indexing\n",
+    "# USER: modify the \"frac\" parameter below and re-run the cell until the orange dot sits nicely on the \"elbow\" of the blue line\n",
+    "# this indicates the fractional intensity cutoff we will select\n",
+    "# if the blue line does not look elbow-shaped in the logscale plot, try changing the \"doplot\" parameter (the y scale of the logscale plot) until it does\n",
     "\n",
-    "cf_strong = utils.selectpeaks(cf_3d, frac=0.95, dsmax=0.92, doplot=0.05, dstol=0.01)\n",
+    "cf_strong = utils.selectpeaks(cf_3d, frac=0.9837, dsmax=0.92, doplot=0.8, dstol=0.01)\n",
     "print(f\"Got {cf_strong.nrows} strong peaks for indexing\")\n",
     "cf_strong.writefile(f'{sample}_{dataset}_3d_peaks_strong.flt')"
    ]
@@ -680,7 +680,7 @@
    "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",
     "# 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\n",
+    "# you can add samples and datasets to skip in skips_dict\n",
     "\n",
     "skips_dict = {\n",
     "    \"FeAu_0p5_tR\": []\n",

diff --git a/ImageD11/nbGui/3DXRD/3_3DXRD_look_at_peaks.ipynb b/ImageD11/nbGui/3DXRD/3_3DXRD_look_at_peaks.ipynb
@@ -17,17 +17,16 @@
    },
    "outputs": [],
    "source": [
-    "# There is a bug with the current version of ImageD11 in the site-wide Jupyter env.\n",
-    "# This has been fixed here: https://github.com/FABLE-3DXRD/ImageD11/commit/4af88b886b1775585e868f2339a0eb975401468f\n",
-    "# Until a new release has been made and added to the env, we need to get the latest version of ImageD11 from GitHub\n",
-    "# Put it in your home directory\n",
     "# USER: Change the path below to point to your local copy of ImageD11:\n",
     "\n",
     "import os\n",
     "\n",
-    "username = os.environ.get(\"USER\")\n",
+    "home_dir = !echo $HOME\n",
+    "home_dir = str(home_dir[0])\n",
     "\n",
-    "id11_code_path = f\"/home/esrf/{username}/Code/ImageD11\"\n",
+    "# USER: You can change this location if you want\n",
+    "\n",
+    "id11_code_path = os.path.join(home_dir, \"Code/ImageD11\")\n",
     "\n",
     "import sys\n",
     "\n",

diff --git a/ImageD11/nbGui/3DXRD/4_3DXRD_merge_slices.ipynb b/ImageD11/nbGui/3DXRD/4_3DXRD_merge_slices.ipynb
@@ -17,17 +17,16 @@
    },
    "outputs": [],
    "source": [
-    "# There is a bug with the current version of ImageD11 in the site-wide Jupyter env.\n",
-    "# This has been fixed here: https://github.com/FABLE-3DXRD/ImageD11/commit/4af88b886b1775585e868f2339a0eb975401468f\n",
-    "# Until a new release has been made and added to the env, we need to get the latest version of ImageD11 from GitHub\n",
-    "# Put it in your home directory\n",
     "# USER: Change the path below to point to your local copy of ImageD11:\n",
     "\n",
     "import os\n",
     "\n",
-    "username = os.environ.get(\"USER\")\n",
+    "home_dir = !echo $HOME\n",
+    "home_dir = str(home_dir[0])\n",
     "\n",
-    "id11_code_path = f\"/home/esrf/{username}/Code/ImageD11\"\n",
+    "# USER: You can change this location if you want\n",
+    "\n",
+    "id11_code_path = os.path.join(home_dir, \"Code/ImageD11\")\n",
     "\n",
     "import sys\n",
     "\n",