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Commit 5251b37f authored by Lafnoune Imane's avatar Lafnoune Imane
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.ipynb_checkpoints/CNN-checkpoint.ipynb 0 → 100644
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.ipynb_checkpoints/CNN_4_images-checkpoint.ipynb 0 → 100644
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.ipynb_checkpoints/CNN_4_images_4channels-checkpoint.ipynb 0 → 100644
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.ipynb_checkpoints/CNN_injection-checkpoint.ipynb 0 → 100644
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.ipynb_checkpoints/Metadata_inspection-checkpoint.ipynb 0 → 100644
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"https://pydicom.github.io/pydicom/stable/tutorials/dataset_basics.html\n",
"Utile pour le rapport:\n",
"http://www.dimitripianeta.fr/documents/traitements/comprendre%20les%20m%C3%A9tadonn%C3%A9es%20.pdf"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"input_directory='../osic-pulmonary-fibrosis-progression'\n",
"patient = 'ID00419637202311204720264'\n",
"image = '10.dcm'\n",
"path = f'{input_directory}/train/{patient}/{image}'"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dataset.file_meta -------------------------------\n",
"(0002, 0000) File Meta Information Group Length UL: 200\n",
"(0002, 0001) File Meta Information Version OB: b'\\x00\\x01'\n",
"(0002, 0002) Media Storage SOP Class UID UI: CT Image Storage\n",
"(0002, 0003) Media Storage SOP Instance UID UI: 2.25.15591725989708101768360543306906204110\n",
"(0002, 0010) Transfer Syntax UID UI: Explicit VR Little Endian\n",
"(0002, 0012) Implementation Class UID UI: 1.2.276.0.7230010.3.0.3.6.1\n",
"(0002, 0013) Implementation Version Name SH: 'OSIRIX_361'\n",
"(0002, 0016) Source Application Entity Title AE: 'ANONYMOUS'\n",
"-------------------------------------------------\n",
"(0008, 0005) Specific Character Set CS: 'ISO_IR 100'\n",
"(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL']\n",
"(0008, 0018) SOP Instance UID UI: 2.25.15591725989708101768360543306906204110\n",
"(0008, 0060) Modality CS: 'CT'\n",
"(0008, 0070) Manufacturer LO: 'PACSGEAR'\n",
"(0008, 1090) Manufacturer's Model Name LO: 'LightSpeed VCT'\n",
"(0010, 0010) Patient's Name PN: 'ID00419637202311204720264'\n",
"(0010, 0020) Patient ID LO: 'ID00419637202311204720264'\n",
"(0010, 0040) Patient's Sex CS: ''\n",
"(0012, 0063) De-identification Method LO: 'Table;'\n",
"(0018, 0015) Body Part Examined CS: 'Chest'\n",
"(0018, 0050) Slice Thickness DS: \"1.25\"\n",
"(0018, 0060) KVP DS: \"120.0\"\n",
"(0018, 1110) Distance Source to Detector DS: \"949.075012\"\n",
"(0018, 1111) Distance Source to Patient DS: \"541.0\"\n",
"(0018, 1120) Gantry/Detector Tilt DS: \"0.0\"\n",
"(0018, 1130) Table Height DS: \"197.0\"\n",
"(0018, 1140) Rotation Direction CS: 'CW'\n",
"(0018, 1151) X-Ray Tube Current IS: \"301\"\n",
"(0018, 1170) Generator Power IS: \"36000\"\n",
"(0018, 1190) Focal Spot(s) DS: \"0.7\"\n",
"(0018, 1210) Convolution Kernel SH: 'BONEPLUS'\n",
"(0018, 5100) Patient Position CS: 'FFS'\n",
"(0020, 000d) Study Instance UID UI: 2.25.24142809421030670533829469959522337181\n",
"(0020, 000e) Series Instance UID UI: 2.25.72922870310959542985933229225637751168\n",
"(0020, 0010) Study ID SH: ''\n",
"(0020, 0013) Instance Number IS: \"10\"\n",
"(0020, 0020) Patient Orientation CS: ''\n",
"(0020, 0032) Image Position (Patient) DS: [-212.600, -170.700, -54.000]\n",
"(0020, 0037) Image Orientation (Patient) DS: [1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000]\n",
"(0020, 0052) Frame of Reference UID UI: 2.25.87733149435852076944786005695371983233\n",
"(0020, 1040) Position Reference Indicator LO: 'SN'\n",
"(0020, 1041) Slice Location DS: \"-54.0\"\n",
"(0028, 0002) Samples per Pixel US: 1\n",
"(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'\n",
"(0028, 0010) Rows US: 1100\n",
"(0028, 0011) Columns US: 888\n",
"(0028, 0030) Pixel Spacing DS: [0.820312, 0.820312]\n",
"(0028, 0100) Bits Allocated US: 16\n",
"(0028, 0101) Bits Stored US: 16\n",
"(0028, 0102) High Bit US: 15\n",
"(0028, 0103) Pixel Representation US: 1\n",
"(0028, 0120) Pixel Padding Value US: 63536\n",
"(0028, 1050) Window Center DS: \"-500.0\"\n",
"(0028, 1051) Window Width DS: \"-1500.0\"\n",
"(0028, 1052) Rescale Intercept DS: \"0.0\"\n",
"(0028, 1053) Rescale Slope DS: \"1.0\"\n",
"(0028, 1054) Rescale Type LO: 'HU'\n",
"(7fe0, 0010) Pixel Data OW: Array of 1953600 elements"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import pydicom\n",
"\n",
"ds = pydicom.filereader.dcmread(path)\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(0018, 1111) Distance Source to Patient DS: \"541.0\""
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"elem = ds[0x0018, 0x1111]\n",
"elem"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'DistanceSourceToPatient'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"elem.keyword"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"541.0\""
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"elem.value"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(0018, 1111) Distance Source to Patient DS: \"541.0\""
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds['DistanceSourceToPatient']"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"541.0\""
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.DistanceSourceToPatient"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.3"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
%% Cell type:markdown id: tags:
https://pydicom.github.io/pydicom/stable/tutorials/dataset_basics.html
Utile pour le rapport:
http://www.dimitripianeta.fr/documents/traitements/comprendre%20les%20m%C3%A9tadonn%C3%A9es%20.pdf
%% Cell type:code id: tags:
``` python
input_directory='../osic-pulmonary-fibrosis-progression'
patient = 'ID00419637202311204720264'
image = '10.dcm'
path = f'{input_directory}/train/{patient}/{image}'
```
%% Cell type:code id: tags:
``` python
import pydicom
ds = pydicom.filereader.dcmread(path)
ds
```
%%%% Output: execute_result
Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length UL: 200
(0002, 0001) File Meta Information Version OB: b'\x00\x01'
(0002, 0002) Media Storage SOP Class UID UI: CT Image Storage
(0002, 0003) Media Storage SOP Instance UID UI: 2.25.15591725989708101768360543306906204110
(0002, 0010) Transfer Syntax UID UI: Explicit VR Little Endian
(0002, 0012) Implementation Class UID UI: 1.2.276.0.7230010.3.0.3.6.1
(0002, 0013) Implementation Version Name SH: 'OSIRIX_361'
(0002, 0016) Source Application Entity Title AE: 'ANONYMOUS'
-------------------------------------------------
(0008, 0005) Specific Character Set CS: 'ISO_IR 100'
(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL']
(0008, 0018) SOP Instance UID UI: 2.25.15591725989708101768360543306906204110
(0008, 0060) Modality CS: 'CT'
(0008, 0070) Manufacturer LO: 'PACSGEAR'
(0008, 1090) Manufacturer's Model Name LO: 'LightSpeed VCT'
(0010, 0010) Patient's Name PN: 'ID00419637202311204720264'
(0010, 0020) Patient ID LO: 'ID00419637202311204720264'
(0010, 0040) Patient's Sex CS: ''
(0012, 0063) De-identification Method LO: 'Table;'
(0018, 0015) Body Part Examined CS: 'Chest'
(0018, 0050) Slice Thickness DS: "1.25"
(0018, 0060) KVP DS: "120.0"
(0018, 1110) Distance Source to Detector DS: "949.075012"
(0018, 1111) Distance Source to Patient DS: "541.0"
(0018, 1120) Gantry/Detector Tilt DS: "0.0"
(0018, 1130) Table Height DS: "197.0"
(0018, 1140) Rotation Direction CS: 'CW'
(0018, 1151) X-Ray Tube Current IS: "301"
(0018, 1170) Generator Power IS: "36000"
(0018, 1190) Focal Spot(s) DS: "0.7"
(0018, 1210) Convolution Kernel SH: 'BONEPLUS'
(0018, 5100) Patient Position CS: 'FFS'
(0020, 000d) Study Instance UID UI: 2.25.24142809421030670533829469959522337181
(0020, 000e) Series Instance UID UI: 2.25.72922870310959542985933229225637751168
(0020, 0010) Study ID SH: ''
(0020, 0013) Instance Number IS: "10"
(0020, 0020) Patient Orientation CS: ''
(0020, 0032) Image Position (Patient) DS: [-212.600, -170.700, -54.000]
(0020, 0037) Image Orientation (Patient) DS: [1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000]
(0020, 0052) Frame of Reference UID UI: 2.25.87733149435852076944786005695371983233
(0020, 1040) Position Reference Indicator LO: 'SN'
(0020, 1041) Slice Location DS: "-54.0"
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0010) Rows US: 1100
(0028, 0011) Columns US: 888
(0028, 0030) Pixel Spacing DS: [0.820312, 0.820312]
(0028, 0100) Bits Allocated US: 16
(0028, 0101) Bits Stored US: 16
(0028, 0102) High Bit US: 15
(0028, 0103) Pixel Representation US: 1
(0028, 0120) Pixel Padding Value US: 63536
(0028, 1050) Window Center DS: "-500.0"
(0028, 1051) Window Width DS: "-1500.0"
(0028, 1052) Rescale Intercept DS: "0.0"
(0028, 1053) Rescale Slope DS: "1.0"
(0028, 1054) Rescale Type LO: 'HU'
(7fe0, 0010) Pixel Data OW: Array of 1953600 elements
%% Cell type:code id: tags:
``` python
elem = ds[0x0018, 0x1111]
elem
```
%%%% Output: execute_result
(0018, 1111) Distance Source to Patient DS: "541.0"
%% Cell type:code id: tags:
``` python
elem.keyword
```
%%%% Output: execute_result
'DistanceSourceToPatient'
%% Cell type:code id: tags:
``` python
elem.value
```
%%%% Output: execute_result
"541.0"
%% Cell type:code id: tags:
``` python
ds['DistanceSourceToPatient']
```
%%%% Output: execute_result
(0018, 1111) Distance Source to Patient DS: "541.0"
%% Cell type:code id: tags:
``` python
ds.DistanceSourceToPatient
```
%%%% Output: execute_result
"541.0"
%% Cell type:code id: tags:
``` python
```
.ipynb_checkpoints/README-checkpoint.md 0 → 100644
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# Projet_FR
https://www.kaggle.com/c/osic-pulmonary-fibrosis-progression
## Set up the environment
Commandes bash pour créer un environnement virtuel, y installer les librairies nécessaires, et le package du projet :
```bash
#create virtual environment
python3 -m venv venvfr
source venvfr/bin/activate
pip install poetry
#install dependencies
cd filrouge/
make build
pip uninstall numpy #answer yes
pip install numpy==1.20.3
#register kernel
python -m ipykernel install --name venvfr
```
on peut alors appeler les fonctions depuis un notebook démarré avec le kernel de l'environnement virtuel:
```bash
from filrouge.preprocessing.read_load_data import *
```
\ No newline at end of file
.ipynb_checkpoints/Regression-checkpoint.ipynb 0 → 100644
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ExploratoryAnalysis/Metadata_inspection.ipynb 0 → 100644
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"https://pydicom.github.io/pydicom/stable/tutorials/dataset_basics.html\n",
"Utile pour le rapport:\n",
"http://www.dimitripianeta.fr/documents/traitements/comprendre%20les%20m%C3%A9tadonn%C3%A9es%20.pdf"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"input_directory='../osic-pulmonary-fibrosis-progression'\n",
"patient = 'ID00419637202311204720264'\n",
"image = '10.dcm'\n",
"path = f'{input_directory}/train/{patient}/{image}'"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dataset.file_meta -------------------------------\n",
"(0002, 0000) File Meta Information Group Length UL: 200\n",
"(0002, 0001) File Meta Information Version OB: b'\\x00\\x01'\n",
"(0002, 0002) Media Storage SOP Class UID UI: CT Image Storage\n",
"(0002, 0003) Media Storage SOP Instance UID UI: 2.25.15591725989708101768360543306906204110\n",
"(0002, 0010) Transfer Syntax UID UI: Explicit VR Little Endian\n",
"(0002, 0012) Implementation Class UID UI: 1.2.276.0.7230010.3.0.3.6.1\n",
"(0002, 0013) Implementation Version Name SH: 'OSIRIX_361'\n",
"(0002, 0016) Source Application Entity Title AE: 'ANONYMOUS'\n",
"-------------------------------------------------\n",
"(0008, 0005) Specific Character Set CS: 'ISO_IR 100'\n",
"(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL']\n",
"(0008, 0018) SOP Instance UID UI: 2.25.15591725989708101768360543306906204110\n",
"(0008, 0060) Modality CS: 'CT'\n",
"(0008, 0070) Manufacturer LO: 'PACSGEAR'\n",
"(0008, 1090) Manufacturer's Model Name LO: 'LightSpeed VCT'\n",
"(0010, 0010) Patient's Name PN: 'ID00419637202311204720264'\n",
"(0010, 0020) Patient ID LO: 'ID00419637202311204720264'\n",
"(0010, 0040) Patient's Sex CS: ''\n",
"(0012, 0063) De-identification Method LO: 'Table;'\n",
"(0018, 0015) Body Part Examined CS: 'Chest'\n",
"(0018, 0050) Slice Thickness DS: \"1.25\"\n",
"(0018, 0060) KVP DS: \"120.0\"\n",
"(0018, 1110) Distance Source to Detector DS: \"949.075012\"\n",
"(0018, 1111) Distance Source to Patient DS: \"541.0\"\n",
"(0018, 1120) Gantry/Detector Tilt DS: \"0.0\"\n",
"(0018, 1130) Table Height DS: \"197.0\"\n",
"(0018, 1140) Rotation Direction CS: 'CW'\n",
"(0018, 1151) X-Ray Tube Current IS: \"301\"\n",
"(0018, 1170) Generator Power IS: \"36000\"\n",
"(0018, 1190) Focal Spot(s) DS: \"0.7\"\n",
"(0018, 1210) Convolution Kernel SH: 'BONEPLUS'\n",
"(0018, 5100) Patient Position CS: 'FFS'\n",
"(0020, 000d) Study Instance UID UI: 2.25.24142809421030670533829469959522337181\n",
"(0020, 000e) Series Instance UID UI: 2.25.72922870310959542985933229225637751168\n",
"(0020, 0010) Study ID SH: ''\n",
"(0020, 0013) Instance Number IS: \"10\"\n",
"(0020, 0020) Patient Orientation CS: ''\n",
"(0020, 0032) Image Position (Patient) DS: [-212.600, -170.700, -54.000]\n",
"(0020, 0037) Image Orientation (Patient) DS: [1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000]\n",
"(0020, 0052) Frame of Reference UID UI: 2.25.87733149435852076944786005695371983233\n",
"(0020, 1040) Position Reference Indicator LO: 'SN'\n",
"(0020, 1041) Slice Location DS: \"-54.0\"\n",
"(0028, 0002) Samples per Pixel US: 1\n",
"(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'\n",
"(0028, 0010) Rows US: 1100\n",
"(0028, 0011) Columns US: 888\n",
"(0028, 0030) Pixel Spacing DS: [0.820312, 0.820312]\n",
"(0028, 0100) Bits Allocated US: 16\n",
"(0028, 0101) Bits Stored US: 16\n",
"(0028, 0102) High Bit US: 15\n",
"(0028, 0103) Pixel Representation US: 1\n",
"(0028, 0120) Pixel Padding Value US: 63536\n",
"(0028, 1050) Window Center DS: \"-500.0\"\n",
"(0028, 1051) Window Width DS: \"-1500.0\"\n",
"(0028, 1052) Rescale Intercept DS: \"0.0\"\n",
"(0028, 1053) Rescale Slope DS: \"1.0\"\n",
"(0028, 1054) Rescale Type LO: 'HU'\n",
"(7fe0, 0010) Pixel Data OW: Array of 1953600 elements"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import pydicom\n",
"\n",
"ds = pydicom.filereader.dcmread(path)\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(0018, 1111) Distance Source to Patient DS: \"541.0\""
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"elem = ds[0x0018, 0x1111]\n",
"elem"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'DistanceSourceToPatient'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"elem.keyword"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"541.0\""
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"elem.value"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(0018, 1111) Distance Source to Patient DS: \"541.0\""
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds['DistanceSourceToPatient']"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"541.0\""
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.DistanceSourceToPatient"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},