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@alexzwanenburg
alexzwanenburg committed Jun 5, 2024
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118 changes: 113 additions & 5 deletions docs_source/source/tutorial_apply_image_filter.ipynb
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"id": "1e447b05-08e1-4326-9709-531acf639a69",
"metadata": {
"editable": true,
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"slideshow": {
"slide_type": ""
},
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"name": "stdout",
"output_type": "stream",
"text": [
"INFO\t: MainProcess \t 2024-04-24 11:26:22,645 \t Initialising image extraction using ct images for 1.\n"
"INFO\t: MainProcess \t 2024-06-05 11:52:36,662 \t Initialising image extraction using ct images for 1.\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"INFO\t: MainProcess \t 2024-04-24 11:26:24,360 \t Initialising image extraction using ct images for 1.\n"
"INFO\t: MainProcess \t 2024-06-05 11:52:38,720 \t Initialising image extraction using ct images for 1.\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 15,
"id": "c211ca72-ad62-491e-86ac-b30ac25ad6b4",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO\t: MainProcess \t 2024-04-24 11:26:40,460 \t Initialising feature computation using ct images for 1.\n"
"INFO\t: MainProcess \t 2024-06-05 11:52:54,562 \t Initialising feature computation using ct images for 1.\n"
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" <th></th>\n",
" <th>sample_name</th>\n",
" <th>image_file_name</th>\n",
" <th>image_directory</th>\n",
" <th>image_study_date</th>\n",
" <th>image_study_description</th>\n",
" <th>image_series_description</th>\n",
" <th>image_series_instance_uid</th>\n",
" <th>image_modality</th>\n",
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" sample_name image_file_name image_directory image_study_date \\\n",
"0 1 None chest_ct\\image None \n",
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" image_study_description image_series_description \\\n",
"0 None None \n",
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" image_series_instance_uid image_modality \\\n",
"0 1.3.6.1.4.1.9590.100.1.2.296658988911737913102... ct \n",
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"0 2.349373e+09 88.482671 \n",
"\n",
"[1 rows x 311 columns]"
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147 changes: 76 additions & 71 deletions docs_source/source/tutorial_compute_radiomics_features_mr.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"INFO\t: MainProcess \t 2024-04-24 11:24:55,664 \t Initialising image extraction using mr images for STS_003.\n"
"INFO\t: MainProcess \t 2024-06-05 11:55:22,262 \t Initialising image extraction using mr images for STS_003.\n"
]
}
],
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"name": "stdout",
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"INFO\t: MainProcess \t 2024-04-24 11:24:57,113 \t Initialising feature computation using mr images for STS_001.\n",
"INFO\t: MainProcess \t 2024-04-24 11:25:10,524 \t Initialising feature computation using mr images for STS_002.\n",
"INFO\t: MainProcess \t 2024-04-24 11:25:19,984 \t Initialising feature computation using mr images for STS_003.\n"
"INFO\t: MainProcess \t 2024-06-05 11:55:23,768 \t Initialising feature computation using mr images for STS_001.\n",
"INFO\t: MainProcess \t 2024-06-05 11:55:36,474 \t Initialising feature computation using mr images for STS_002.\n",
"INFO\t: MainProcess \t 2024-06-05 11:55:46,159 \t Initialising feature computation using mr images for STS_003.\n"
]
},
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" <th>image_voxel_size_y</th>\n",
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" <th>image_noise_level</th>\n",
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" <td>685.643163</td>\n",
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" <td>232.044296</td>\n",
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" <td>MRI PELVIS C- C</td>\n",
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Expand All @@ -653,51 +653,56 @@
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"text/plain": [
" sample_name image_settings_id image_modality image_voxel_size_x \\\n",
"0 STS_001 mr 1.0 \n",
"0 STS_002 mr 1.0 \n",
"0 STS_003 mr 1.0 \n",
" sample_name image_file_name image_directory \\\n",
"0 STS_001 None sts_images\\STS_001\\mr_t1\\image \n",
"0 STS_002 None sts_images\\STS_002\\mr_t1\\image \n",
"0 STS_003 None sts_images\\STS_003\\mr_t1\\image \n",
"\n",
" image_study_date image_study_description image_series_description \\\n",
"0 20000903 ^THIGH AXIAL SE T1 - RESEARCH \n",
"0 20060103 L-SPINE AXT1 \n",
"0 20050330 MRI PELVIS C- C AX T1 \n",
"\n",
" image_voxel_size_y image_voxel_size_z image_noise_level \\\n",
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" image_series_instance_uid image_modality \\\n",
"0 1.3.6.1.4.1.14519.5.2.1.5168.1900.236909650266... mr \n",
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"0 1.3.6.1.4.1.14519.5.2.1.5168.1900.900154069973... mr \n",
"\n",
" image_noise_iteration_id image_rotation_angle image_translation_x ... \\\n",
"0 NaN 0.0 0.0 ... \n",
"0 NaN 0.0 0.0 ... \n",
"0 NaN 0.0 0.0 ... \n",
" image_pet_suv_type image_mask_label ... ngl_hdhge_d1_a0.0_2d_fbn_n16 \\\n",
"0 None GTV_Mass ... 649.904779 \n",
"0 None GTV_Mass ... 731.317187 \n",
"0 None GTV_Mass ... 608.689328 \n",
"\n",
" ngl_hdhge_d1_a0.0_2d_fbn_n16 ngl_glnu_d1_a0.0_2d_fbn_n16 \\\n",
"0 649.904779 685.643163 \n",
"0 731.317187 232.044296 \n",
"0 608.689328 472.701740 \n",
" ngl_glnu_d1_a0.0_2d_fbn_n16 ngl_glnu_norm_d1_a0.0_2d_fbn_n16 \\\n",
"0 685.643163 0.202679 \n",
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"0 472.701740 0.345461 \n",
"\n",
" ngl_glnu_norm_d1_a0.0_2d_fbn_n16 ngl_dcnu_d1_a0.0_2d_fbn_n16 \\\n",
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"0 0.208755 212.059230 \n",
"0 0.345461 334.257475 \n",
" ngl_dcnu_d1_a0.0_2d_fbn_n16 ngl_dcnu_norm_d1_a0.0_2d_fbn_n16 \\\n",
"0 573.379973 0.164149 \n",
"0 212.059230 0.183419 \n",
"0 334.257475 0.238191 \n",
"\n",
" ngl_dcnu_norm_d1_a0.0_2d_fbn_n16 ngl_dc_perc_d1_a0.0_2d_fbn_n16 \\\n",
"0 0.164149 1.0 \n",
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" ngl_dc_perc_d1_a0.0_2d_fbn_n16 ngl_gl_var_d1_a0.0_2d_fbn_n16 \\\n",
"0 1.0 2.124407 \n",
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"0 1.0 3.232402 \n",
"\n",
" ngl_gl_var_d1_a0.0_2d_fbn_n16 ngl_dc_var_d1_a0.0_2d_fbn_n16 \\\n",
"0 2.124407 2.835808 \n",
"0 3.301315 5.169630 \n",
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" ngl_dc_var_d1_a0.0_2d_fbn_n16 ngl_dc_entr_d1_a0.0_2d_fbn_n16 \\\n",
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"0 5.048137 0.050158 \n",
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"\n",
"[3 rows x 192 columns]"
"[3 rows x 203 columns]"
]
},
"execution_count": 7,
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