papermill tests take a command line arg to give the output folder destination

ImageD11/nbGui/S3DXRD/0_segment_and_label.ipynb

@@ -20,18 +20,6 @@
     "Outside ESRF: download [install_ImageD11_from_git.py](https://github.com/FABLE-3DXRD/ImageD11/tree/master/ImageD11/nbGui/install_ImageD11_from_git.py), and update the path in the next cell:"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "fbd76936-7fac-4b03-99eb-2e1651ac4dd5",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -51,13 +39,17 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
+    "PYTHONPATH = None\n",
     "\n",
     "# Experts : update these files for your detector if you need to\n",
-    "maskfile = \"/data/id11/nanoscope/Eiger/eiger_mask_E-08-0144_20240205.edf\"\n",
-    "# e2dxfile = \"/data/id11/nanoscope/Eiger/e2dx_E-08-0144_20240205.edf\"\n",
-    "# e2dyfile = \"/data/id11/nanoscope/Eiger/e2dy_E-08-0144_20240205.edf\"\n",
+    "maskfile = \"/data/id11/nanoscope/Eiger/eiger_mask_E-08-0144_20250819.edf\"\n",
+    "# old papermill tests still use e2dx + e2dy\n",
+    "#  if you give e2dxfile, this is used. Otherwise it takes the detector h5 below.\n",
+    "e2dxfile = None # \"/data/id11/nanoscope/Eiger/e2dx_E-08-0144_20240205.edf\"\n",
+    "e2dyfile = None # \"/data/id11/nanoscope/Eiger/e2dy_E-08-0144_20240205.edf\"\n",
+    "# For the future easier to have one detectorh5 (so you can't mix up x/y).\n",
     "detectorh5 = \"/data/id11/nanoscope/Eiger/spatial_20250826_LJ/newSpatial_20250819.h5\"\n",
     "detector = 'eiger'\n",
     "omegamotor = 'rot_center'\n",
@@ -88,7 +80,9 @@
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    PYTHONPATH=setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {
@@ -217,8 +211,11 @@
     "                                       )\n",
     "ds.import_all()  # Can use scans = [f'{scan}.1' for scan in range(1,102)] )\n",
     "ds.maskfile = maskfile\n",
-    "ds.e2dxfile = e2dxfile\n",
-    "ds.e2dyfile = e2dyfile\n",
+    "if e2dxfile is not None:\n",
+    "    ds.e2dxfile = e2dxfile\n",
+    "    ds.e2dyfile = e2dyfile\n",
+    "else:\n",
+    "    ds.detectorh5 = detectorh5\n",
     "ds.save()"
    ]
   },

ImageD11/nbGui/S3DXRD/0_segment_frelon.ipynb

@@ -32,18 +32,6 @@
     "It will automatically download and install ImageD11 to your home directory"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2402147c-5513-4907-8ca9-76e3e252df0c",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -63,8 +51,8 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "# Experts : update these files for your detector if you need to\n",
     "\n",
@@ -110,17 +98,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ac4e7e05-93ac-4ffc-849f-9bc581889911",
+   "id": "2402147c-5513-4907-8ca9-76e3e252df0c",
    "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
     "tags": []
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/S3DXRD/4_visualise.ipynb

@@ -41,15 +41,6 @@
     "os.environ['MKL_NUM_THREADS'] = '1'"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -68,8 +59,8 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "# dataset file to import\n",
     "dset_path = 'si_cube_test/processed/Si_cube/Si_cube_S3DXRD_nt_moves_dty/Si_cube_S3DXRD_nt_moves_dty_dataset.h5'\n",
@@ -84,16 +75,12 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/S3DXRD/5_combine_phases.ipynb

@@ -16,16 +16,6 @@
     "__Date: 21/02/2025__"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "636849a2-54fd-44ce-aca3-cb8e7e945e59",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -45,8 +35,8 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "# dataset file to import\n",
     "dset_path = 'si_cube_test/processed/Si_cube/Si_cube_S3DXRD_nt_moves_dty/Si_cube_S3DXRD_nt_moves_dty_dataset.h5'\n",
@@ -70,7 +60,9 @@
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/S3DXRD/6_run_papermill.ipynb

@@ -58,8 +58,8 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "# give it a path to an existing dataset to determine the required paths\n",
     "dset_path = \"path/to/dataset.h5\"\n",
@@ -91,7 +91,9 @@
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/S3DXRD/7_stack_layers.ipynb

@@ -49,8 +49,8 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "# supply the path to one dataset file - we'll find the rest automatically\n",
     "dset_path = 'si_cube_test/processed/Si_cube/Si_cube_S3DXRD_nt_moves_dty/Si_cube_S3DXRD_nt_moves_dty_dataset.h5'\n",
@@ -81,7 +81,9 @@
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/S3DXRD/fit_y0.ipynb

@@ -44,8 +44,8 @@
    "outputs": [],
    "source": [
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "dset_path = 'si_cube_test/processed/Si_cube/Si_cube_S3DXRD_nt_moves_dty/Si_cube_S3DXRD_nt_moves_dty_dataset.h5'\n",
     "\n",
@@ -65,7 +65,9 @@
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/S3DXRD/friedel_pair_map.ipynb

@@ -22,21 +22,6 @@
     "Jon Wright. March 2025.\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -50,8 +35,8 @@
    "outputs": [],
    "source": [
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"\n",
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout\n",
     "\n",
     "\n",
     "dset_path = \"/path/to/dataset\"\n",
@@ -78,6 +63,23 @@
     "    ytol = 2."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

ImageD11/nbGui/S3DXRD/import_test_data.ipynb

@@ -31,16 +31,6 @@
     "It will automatically download and install ImageD11 to your home directory\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6f943f39-15ab-4bda-b0d9-38ed46f06b5a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -60,8 +50,20 @@
     "# to view the tag, select the cell, then find the settings gear icon (right or left sidebar) and look for Cell Tags\n",
     "download_dir = 'si_cube_test'\n",
     "# python environment stuff\n",
-    "CHECKOUT_PATH = None\n",
-    "IMAGED11_PATH = \"ImageD11\"    # Name of the git checkout folder"
+    "IMAGED11_PATH = None  # means do not use git, otherwise \"ImageD11\" or \"ImageD11_version_xx\", etc\n",
+    "CHECKOUT_PATH = None  # None means guess, or you can specify a folder for the checkout"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6f943f39-15ab-4bda-b0d9-38ed46f06b5a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if IMAGED11_PATH is not None:\n",
+    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "    setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {
@@ -77,8 +79,6 @@
    },
    "outputs": [],
    "source": [
-    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)\n",
-    "\n",
     "import os\n",
     "\n",
     "import ImageD11.sinograms.dataset\n",