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JeanBilheuxJeanBilheux
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fixed bug. this refs #316 
1 parent cbdc65f commit eb741f9

3 files changed

Lines changed: 289 additions & 18 deletions

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‎notebooks/__code/_utilities/images.py‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
11
import dxchange
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import numpy as np
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from tqdm import tqdm
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from skimage.io import imread
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import multiprocessing as mp
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def _init_arr_from_stack(list_files, ext=".tiff", slc=None):
@@ -40,3 +42,18 @@ def read_img_stack(list_files: list, ext=".tiff", fliplr=False, flipud=False):
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_arr = np.flipud(_arr)
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arr[m] = _arr
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return arr
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def _worker(fl):
48+
return (imread(fl).astype(np.float32)).swapaxes(0, 1)
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def load_data_using_multithreading(list_tif: list = None, combine_tof: bool = False) -> np.ndarray:
52+
"""load data using multithreading"""
53+
with mp.Pool(processes=40) as pool:
54+
data = pool.map(_worker, list_tif)
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56+
if combine_tof:
57+
return np.array(data).sum(axis=0)
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else:
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return np.array(data, dtype=np.float32)

‎notebooks/__code/mcp_chips_corrector/mcp_chips_corrector.py‎

Lines changed: 3 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
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import numpy as np
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from IPython.display import HTML, display
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from NeuNorm.normalization import Normalization
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# from NeuNorm.normalization import Normalization
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from __code._utilities.images import load_data_using_multithreading
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from __code.ipywe import fileselector
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@@ -33,12 +33,9 @@ def load_data(self, folder_selected):
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working_list_files = [file for file in full_list_files if "_SummedImg.fits" not in file]
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o_norm = Normalization()
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o_norm.load(file=working_list_files, notebook=True)
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self.working_data = load_data_using_multithreading(list_tif=working_list_files)
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self.input_working_folder = folder_selected
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self.working_list_files = working_list_files
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self.working_data = o_norm.data["sample"]["data"]
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# create integrated data set
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self.integrated_data = np.sum(self.working_data, axis=0)

‎notebooks/mcp_chips_corrector.ipynb‎

Lines changed: 269 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -23,22 +23,228 @@
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},
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"run_control": {
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"read_only": false
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}
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},
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"outputs": [],
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"olefile module not found\n"
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]
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},
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{
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"data": {
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"</style>\n"
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"text/plain": [
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"<IPython.core.display.HTML object>"
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" by Aron Ahmadia and David Ketcheson and has been reused under CC BY 4.0\n",
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"\n",
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"/* main background */\n",
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"#site {\n",
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" background: #888;\n",
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"div.cell { /* set cell width to about 80 chars */\n",
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" width: 95%;\n",
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"}\n",
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"\n",
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"div #notebook { /* centre the content */\n",
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"/* background: #fff; /* white background for content */\n",
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" background: blue;\n",
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" width: 100%;\n",
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"#notebook li { /* More space between bullet points */\n",
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" background-color: green;\n",
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"}\n",
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150+
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151+
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"\tfont-family: Arial, 'Helvetica Neue', Helvetica, sans-serif;\n",
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".text_cell_render h3 {\n",
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"\tfont-family: Arial, 'Helvetica Neue', Helvetica, sans-serif;\n",
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" margin-top:12px;\n",
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" font-style: italic;\n",
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" margin-bottom: 1px;\n",
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" margin-top: 1px;\n",
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"}\n",
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"\n",
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".CodeMirror{\n",
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" font-family: \"PT Mono\", fixed;\n",
219+
" font-size: 100%;\n",
220+
"}\n",
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"\n",
222+
"#notebook_panel { /* main background */\n",
223+
" background-image: url(\"tile_background.jpg\");\n",
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"}\n",
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"\n",
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"\n",
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"\n",
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"\n",
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"</style>\n"
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],
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"text/plain": [
232+
"<IPython.core.display.HTML object>"
233+
]
234+
},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
34240
"source": [
35241
"import warnings\n",
36242
"warnings.filterwarnings('ignore')\n",
37243
"\n",
38244
"from __code import system\n",
39245
"from __code.mcp_chips_corrector.mcp_chips_corrector import McpChipsCorrector\n",
40246
"from __code.mcp_chips_corrector.interface import Interface\n",
41-
"system.System.select_working_dir(notebook='mcp_chips_corrector')\n",
247+
"system.System.select_working_dir(notebook='mcp_chips_corrector', instrument=\"VENUS\", ipts=\"IPTS-33699\")\n",
42248
"from __code.__all import custom_style\n",
43249
"custom_style.style()"
44250
]
@@ -52,8 +258,16 @@
52258
},
53259
{
54260
"cell_type": "code",
55-
"execution_count": null,
56-
"metadata": {},
261+
"execution_count": 2,
262+
"metadata": {
263+
"execution": {
264+
"iopub.execute_input": "2026-01-15T13:38:37.459175Z",
265+
"iopub.status.busy": "2026-01-15T13:38:37.458752Z",
266+
"iopub.status.idle": "2026-01-15T13:38:37.530655Z",
267+
"shell.execute_reply": "2026-01-15T13:38:37.529973Z",
268+
"shell.execute_reply.started": "2026-01-15T13:38:37.459160Z"
269+
}
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},
57271
"outputs": [],
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"source": [
59273
"%gui qt"
@@ -73,14 +287,36 @@
73287
},
74288
{
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"cell_type": "code",
76-
"execution_count": null,
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"execution_count": 3,
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"metadata": {
292+
"execution": {
293+
"iopub.execute_input": "2026-01-15T13:38:40.428955Z",
294+
"iopub.status.busy": "2026-01-15T13:38:40.428790Z",
295+
"iopub.status.idle": "2026-01-15T13:38:40.444112Z",
296+
"shell.execute_reply": "2026-01-15T13:38:40.443533Z",
297+
"shell.execute_reply.started": "2026-01-15T13:38:40.428942Z"
298+
},
78299
"run_control": {
79300
"frozen": false,
80301
"read_only": false
81302
}
82303
},
83-
"outputs": [],
304+
"outputs": [
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{
306+
"data": {
307+
"application/vnd.jupyter.widget-view+json": {
308+
"model_id": "4ff99133e5064584bc727901ba24fe28",
309+
"version_major": 2,
310+
"version_minor": 0
311+
},
312+
"text/plain": [
313+
"VBox(children=(HTML(value=\"<b><font color='green'>Select MCP Folder ...</b>\"), VBox(children=(HBox(children=(H…"
314+
]
315+
},
316+
"metadata": {},
317+
"output_type": "display_data"
318+
}
319+
],
84320
"source": [
85321
"o_corrector = McpChipsCorrector(working_dir = system.System.get_working_dir())\n",
86322
"o_corrector.select_folder()"
@@ -95,9 +331,30 @@
95331
},
96332
{
97333
"cell_type": "code",
98-
"execution_count": null,
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"metadata": {},
100-
"outputs": [],
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"execution_count": 4,
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"metadata": {
336+
"execution": {
337+
"iopub.execute_input": "2026-01-15T13:39:22.518890Z",
338+
"iopub.status.busy": "2026-01-15T13:39:22.518671Z",
339+
"iopub.status.idle": "2026-01-15T13:39:24.144699Z",
340+
"shell.execute_reply": "2026-01-15T13:39:24.144036Z",
341+
"shell.execute_reply.started": "2026-01-15T13:39:22.518871Z"
342+
}
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},
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"outputs": [
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{
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"data": {
347+
"text/html": [
348+
"<span style=\"font-size: 20px; color:blue\">Check UI that popped up (maybe hidden behind this browser!)</span>"
349+
],
350+
"text/plain": [
351+
"<IPython.core.display.HTML object>"
352+
]
353+
},
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"metadata": {},
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"output_type": "display_data"
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}
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],
101358
"source": [
102359
"o_interface = Interface(o_corrector=o_corrector)\n",
103360
"o_interface.show()"
@@ -128,7 +385,7 @@
128385
"name": "python",
129386
"nbconvert_exporter": "python",
130387
"pygments_lexer": "ipython3",
131-
"version": "3.10.8"
388+
"version": "3.12.12"
132389
},
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"toc": {
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"colors": {
@@ -151,5 +408,5 @@
151408
}
152409
},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
155412
}

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