Merge branch '6-py-bkg-rm' of https://gitlab.esrf.fr/graintracking/dct into 6-py-bkg-rm

5e02d370 · casagran · 199c5aef · fb3b6092 · 5e02d370 · 5e02d370
Commit 5e02d370 authored 3 years ago by casagran
--- a/zUtil_Python/pydct/dev/qt-window.ipynb
+++ b/zUtil_Python/pydct/dev/qt-window.ipynb
@@ -380,7 +380,7 @@
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-   "version": "3.9.4"
+   "version": "3.9.5"
  }
 },
 "nbformat": 4,

--- a/zUtil_Python/pydct/dev/scratches/reduce-ET11.ipynb
+++ b/zUtil_Python/pydct/dev/scratches/reduce-ET11.ipynb
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "aa5dea9f-c037-4f52-a1e0-78c1f68f5361",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from silx.io import get_data\n",
+    "from silx.io.dictdump import dicttoh5"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "3b211988-44b8-4b3d-975e-9bd4f638a52d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/home/kscroot/data/ET11_3_dct_0_z0_\n"
+     ]
+    }
+   ],
+   "source": [
+    "%cd ~/data/ET11_3_dct_0_z0_/"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "0073c304-c532-4f8e-8a07-d3e285ae80ab",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "ET11_3_dct_0_z0_.nxs      ET11_3_dct_0_z0_.par.md5  pre_ref.nxs.md5\n",
+      "ET11_3_dct_0_z0_.nxs.md5  post_dark.nxs.md5\n",
+      "ET11_3_dct_0_z0_.par      post_ref.nxs.md5\n"
+     ]
+    }
+   ],
+   "source": [
+    "%ls"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "baf032c0-3d3e-41cf-9e40-e804269a6179",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "d1606a28-fb62-46b6-861d-89f539daf283",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "filepath = Path(\".\") / \"ET11_3_dct_0_z0_.nxs\"\n",
+    "datalink = \"/flyscan_00001/scan_data/orca_image\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "6841f3d3-f2c2-4c64-94e8-3468cb5b0b75",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = get_data(f\"silx:{str(filepath)}::{datalink}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "54a37ca1-29ab-4107-8c4d-ec9517c11a50",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(3600, 2048, 2048)"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "data.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "3f7e3203-b013-49bb-8505-7b09ca8ba325",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reduced = data[:60]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "dd22f2d7-e0cc-47e9-87f2-524b932d1ce5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reduced_datalink = \"/reduced\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "fdd70dc0-27ff-475b-aa15-d7e63aae0661",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dicttoh5(\n",
+    "    dict(raw=reduced),\n",
+    "    str(filepath),\n",
+    "    reduced_datalink,\n",
+    "    mode=\"a\",\n",
+    "    update_mode=\"add\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "600a505c-b621-4276-9720-7e9920a3e8cd",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/home/kscroot/data/ET11_3_dct_0_z0_'"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "%pwd"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "id": "5ba72298-2ab1-4b1e-af72-1639e651e473",
+   "metadata": {},
+   "source": [
+    "url to the reduced data"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "id": "649c0588-016f-40b0-afa0-b495bf1d1f27",
+   "metadata": {},
+   "source": [
+    "silx:/home/kscroot/data/ET11_3_dct_0_z0_/ET11_3_dct_0_z0_.nxs::/reduced/raw"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7f9adb80-b3a5-434b-85bc-0b61e5e5c710",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pydct-dev",
+   "language": "python",
+   "name": "pydct-dev"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
+%% Cell type:code id:aa5dea9f-c037-4f52-a1e0-78c1f68f5361 tags:
+
+``` python
+from silx.io import get_data
+from silx.io.dictdump import dicttoh5
+```
+
+%% Cell type:code id:3b211988-44b8-4b3d-975e-9bd4f638a52d tags:
+
+``` python
+%cd ~/data/ET11_3_dct_0_z0_/
+```
+
+%% Output
+
+    /home/kscroot/data/ET11_3_dct_0_z0_
+
+%% Cell type:code id:0073c304-c532-4f8e-8a07-d3e285ae80ab tags:
+
+``` python
+%ls
+```
+
+%% Output
+
+    ET11_3_dct_0_z0_.nxs      ET11_3_dct_0_z0_.par.md5  pre_ref.nxs.md5
+    ET11_3_dct_0_z0_.nxs.md5  post_dark.nxs.md5
+    ET11_3_dct_0_z0_.par      post_ref.nxs.md5
+
+%% Cell type:code id:baf032c0-3d3e-41cf-9e40-e804269a6179 tags:
+
+``` python
+from pathlib import Path
+```
+
+%% Cell type:code id:d1606a28-fb62-46b6-861d-89f539daf283 tags:
+
+``` python
+filepath = Path(".") / "ET11_3_dct_0_z0_.nxs"
+datalink = "/flyscan_00001/scan_data/orca_image"
+```
+
+%% Cell type:code id:6841f3d3-f2c2-4c64-94e8-3468cb5b0b75 tags:
+
+``` python
+data = get_data(f"silx:{str(filepath)}::{datalink}")
+```
+
+%% Cell type:code id:54a37ca1-29ab-4107-8c4d-ec9517c11a50 tags:
+
+``` python
+data.shape
+```
+
+%% Output
+
+    (3600, 2048, 2048)
+
+%% Cell type:code id:3f7e3203-b013-49bb-8505-7b09ca8ba325 tags:
+
+``` python
+reduced = data[:60]
+```
+
+%% Cell type:code id:dd22f2d7-e0cc-47e9-87f2-524b932d1ce5 tags:
+
+``` python
+reduced_datalink = "/reduced"
+```
+
+%% Cell type:code id:fdd70dc0-27ff-475b-aa15-d7e63aae0661 tags:
+
+``` python
+dicttoh5(
+    dict(raw=reduced),
+    str(filepath),
+    reduced_datalink,
+    mode="a",
+    update_mode="add",
+)
+```
+
+%% Cell type:code id:600a505c-b621-4276-9720-7e9920a3e8cd tags:
+
+``` python
+%pwd
+```
+
+%% Output
+
+    '/home/kscroot/data/ET11_3_dct_0_z0_'
+
+%% Cell type:raw id:5ba72298-2ab1-4b1e-af72-1639e651e473 tags:
+
+url to the reduced data
+
+%% Cell type:raw id:649c0588-016f-40b0-afa0-b495bf1d1f27 tags:
+
+silx:/home/kscroot/data/ET11_3_dct_0_z0_/ET11_3_dct_0_z0_.nxs::/reduced/raw
+
+%% Cell type:code id:7f9adb80-b3a5-434b-85bc-0b61e5e5c710 tags:
+
+``` python
+```
--- a/zUtil_Python/pydct/dev/reduce-marana00.ipynb
+++ b/zUtil_Python/pydct/dev/reduce-marana00.ipynb
--- a/zUtil_Python/pydct/pydct/preprocess/preprocess_aux.py
+++ b/zUtil_Python/pydct/pydct/preprocess/preprocess_aux.py
+#from enum 
+
+
--- a/zUtil_Python/pydct/pydct/preprocess/untitled.txt
+++ b/zUtil_Python/pydct/pydct/preprocess/untitled.txt
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z0_ .
+
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z0_/post_dark.nxs . && \
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z0_/post_ref.nxs . && \
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z0_/pre_ref.nxs .
+
+mkdir ET11_3_dct_0_z1_ && scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z1_/* ET11_3_dct_0_z1_
+
+
+
+
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z0_.tar.gz . && \
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z1_.tar.gz . && \
+scp com-psiche@195.221.7.39:/nfs/ruche-psiche/psiche-soleil/com-psiche/proposal/2020/Proudhon_0320/ET11_3_dct_0_z2_.tar.gz .