Mise à jour Imane Branch

5251b37f · Lafnoune Imane · a1578b94 · 5251b37f · 5251b37f · 5251b37f
Commit 5251b37f authored May 19, 2021 by Lafnoune Imane
--- a/.ipynb_checkpoints/CNN-checkpoint.ipynb
+++ b/.ipynb_checkpoints/CNN-checkpoint.ipynb
--- a/.ipynb_checkpoints/CNN_4_images-checkpoint.ipynb
+++ b/.ipynb_checkpoints/CNN_4_images-checkpoint.ipynb
--- a/.ipynb_checkpoints/CNN_4_images_4channels-checkpoint.ipynb
+++ b/.ipynb_checkpoints/CNN_4_images_4channels-checkpoint.ipynb
--- a/.ipynb_checkpoints/CNN_injection-checkpoint.ipynb
+++ b/.ipynb_checkpoints/CNN_injection-checkpoint.ipynb
--- a/.ipynb_checkpoints/Metadata_inspection-checkpoint.ipynb
+++ b/.ipynb_checkpoints/Metadata_inspection-checkpoint.ipynb
+%% 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
+
+```
--- a/.ipynb_checkpoints/README-checkpoint.md
+++ b/.ipynb_checkpoints/README-checkpoint.md
+# 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
--- a/.ipynb_checkpoints/Regression-checkpoint.ipynb
+++ b/.ipynb_checkpoints/Regression-checkpoint.ipynb
--- a/.ipynb_checkpoints/imane-checkpoint.ipynb
+++ b/.ipynb_checkpoints/imane-checkpoint.ipynb
--- a/.ipynb_checkpoints/k-fold-efficientnet-models-checkpoint.ipynb
+++ b/.ipynb_checkpoints/k-fold-efficientnet-models-checkpoint.ipynb
--- a/.ipynb_checkpoints/k-fold-efficientnet-models-training-checkpoint.ipynb
+++ b/.ipynb_checkpoints/k-fold-efficientnet-models-training-checkpoint.ipynb
--- a/DICOM_Metadata.csv
+++ b/DICOM_Metadata.csv
--- a/DICOM_Metadata.pkl
+++ b/DICOM_Metadata.pkl
--- a/DICOM_Metadata_full.csv
+++ b/DICOM_Metadata_full.csv
--- a/DICOM_Metadata_full.pkl
+++ b/DICOM_Metadata_full.pkl
--- a/ExploratoryAnalysis/Metadata_inspection.ipynb
+++ b/ExploratoryAnalysis/Metadata_inspection.ipynb
+%% 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
+
+```
--- a/metadata_analysis.ipynb
+++ b/metadata_analysis.ipynb
--- a/projet-fr.ipynb
+++ b/projet-fr.ipynb
--- a/README.md
+++ b/README.md
 # Projet_FR
-Amelie
+
+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
--- a/clean_notebooks/CNN_collage_1Chann.ipynb
+++ b/clean_notebooks/CNN_collage_1Chann.ipynb
--- a/clean_notebooks/CNN_injection_collage_1Chann.ipynb
+++ b/clean_notebooks/CNN_injection_collage_1Chann.ipynb