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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/s184058/.conda/envs/qim/lib/python3.10/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension: 'libc10_cuda.so: cannot open shared object file: No such file or directory'If you don't plan on using image functionality from `torchvision.io`, you can ignore this warning. Otherwise, there might be something wrong with your environment. Did you have `libjpeg` or `libpng` installed before building `torchvision` from source?\n",
" warn(\n",
"astropy module not found\n"
]
}
],
"source": [
"import qim3d\n",
"import dxchange\n",
"import olefile\n",
"import compoundfiles\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"import os\n",
"import struct\n",
"import sys"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"qim3d.io.logger.set_level_info()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"txrm_file = 'data/glasfiber_test_4X-40kV-LE3-15s-5p6micro.txrm'\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Offsets are not ascending, some slices are erroneous\n",
"Loaded shape: (1601, 1014, 1014)\n",
"Using 3.1 GB of memory\n",
"Offsets are not ascending, some slices are erroneous\n",
"Loaded shape: (1601, 1014, 1014)\n",
"Using 80.0 B of memory\n"
]
}
],
"source": [
"vol, _ = qim3d.io.load(txrm_file,virtual_stack=False)\n",
"vol_mm, offsets = qim3d.io.load(txrm_file,virtual_stack=True) # return offset temporarily to explore issue"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
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