Compute Radiomics#
In this example notebook we use PyRadiomics to compute various type of radiomics features. We use some LCTSC data from the Cancer Imaging Archive which has already been converted using PyDicer for demonstration purposes.
[1]:
try:
from pydicer import PyDicer
except ImportError:
!pip install pydicer
from pydicer import PyDicer
from pathlib import Path
from pydicer.utils import fetch_converted_test_data
from pydicer.utils import load_object_metadata
Fetch data#
LCTSC data prepared for this example are downloaded and stored into a testdata_lctsc directory. We will use this for our PyDicer working directory.
[2]:
working_directory = fetch_converted_test_data("./testdata_lctsc", dataset="LCTSC")
Working directory %s aready exists, won't download test data.
Initialise PyDicer object#
Using the working directory containing the LCTSC test data.
[3]:
pydicer = PyDicer(working_directory)
Compute Default Radiomics#
By default, PyDicer will compute only first-order radiomics features. Radiomics are computed for each structure available in the dataset using the image data of images linked to those structures.
[4]:
pydicer.analyse.compute_radiomics()
pydicer.analyse.data - INFO - Computing radiomics for structure set ed6686 and image 5adf40
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set ceb111 and image 88c5ef
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 6c6ea4 and image 914d57
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set f036b8 and image aa38e6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Right
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Left
pydicer.analyse.data - INFO - Computing radiomics for structure set 48a970 and image dd0026
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 61758b and image d91c84
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SC
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 68d663 and image 738c1a
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure L_Lung
pydicer.analyse.data - INFO - Computing radiomics for structure set b5bddb and image 6834c9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set cc682f and image 666be6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 8e34f9 and image 2bf2f9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
Fetch computed Radiomics#
Use the get_all_computed_radiomics_for_dataset function to fetch all radiomics features computed in the last step.
The .head() function on a Pandas DataFrame output the first 5 rows for inspection.
[5]:
# Display the DataFrame of radiomics computed
df_radiomics = pydicer.analyse.get_all_computed_radiomics_for_dataset()
df_radiomics.head()
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
[5]:
| Contour | Patient | ImageHashedUID | StructHashedUID | ResampledPixelSpacing | NormalisationScale | firstorder|10Percentile | firstorder|90Percentile | firstorder|Energy | firstorder|Entropy | ... | firstorder|Mean | firstorder|Median | firstorder|Minimum | firstorder|Range | firstorder|RobustMeanAbsoluteDeviation | firstorder|RootMeanSquared | firstorder|Skewness | firstorder|TotalEnergy | firstorder|Uniformity | firstorder|Variance | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Esophagus | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -9.0 | 74.0 | 6.379739e+06 | 2.563380 | ... | 33.382764 | 42.0 | -745.0 | 940.0 | 15.951183 | 70.379070 | -5.961993 | 1.642731e+08 | 0.232723 | 3838.804579 |
| 4 | Heart | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -14.0 | 68.0 | 8.486142e+07 | 2.343017 | ... | 34.078823 | 44.0 | -577.0 | 806.0 | 14.250737 | 53.881633 | -2.753651 | 2.185112e+09 | 0.273513 | 1741.864194 |
| 0 | Lung_L | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -871.0 | -502.0 | 3.907161e+10 | 4.313815 | ... | -729.756106 | -778.0 | -1000.0 | 1357.0 | 67.906500 | 747.249117 | 1.747786 | 1.006062e+12 | 0.069585 | 25837.268599 |
| 2 | Lung_R | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -889.0 | -480.0 | 4.790689e+10 | 4.414603 | ... | -735.842185 | -789.0 | -1000.0 | 1215.0 | 76.876692 | 755.465238 | 1.617379 | 1.233563e+12 | 0.063675 | 29264.004413 |
| 3 | SpinalCord | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -19.0 | 70.0 | 6.830546e+06 | 2.638360 | ... | 27.051730 | 27.0 | -144.0 | 573.0 | 18.213519 | 49.364661 | 1.348291 | 1.758810e+08 | 0.205445 | 1705.073671 |
5 rows × 24 columns
Specify Radiomics to Compute#
PyDicer used the popular pyradiomics library to compute radiomics. So, you may specify any radiomics features provided in that library to be computed. See the pyradiomics documentation for a list of radiomics features available.
In this example, we specify all shape features as well as first-order features to be computed.
[6]:
# Import pyradiomics feature modules
from radiomics import (
firstorder,
shape,
)
# Prepare a dict of features to compute grouped by class
first_order_features = firstorder.RadiomicsFirstOrder.getFeatureNames()
shape_features = shape.RadiomicsShape.getFeatureNames()
compute_radiomics = {
"firstorder": [f for f in first_order_features if not first_order_features[f]],
"shape": [f for f in shape_features if not shape_features[f]],
}
# Pass the dict to the compute the radiomics
pydicer.analyse.compute_radiomics(radiomics=compute_radiomics)
# Fetch the computed radiomics and output the first few rows
df_radiomics = pydicer.analyse.get_all_computed_radiomics_for_dataset()
df_radiomics.head()
pydicer.analyse.data - INFO - Computing radiomics for structure set ed6686 and image 5adf40
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set ceb111 and image 88c5ef
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 6c6ea4 and image 914d57
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set f036b8 and image aa38e6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Right
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Left
pydicer.analyse.data - INFO - Computing radiomics for structure set 48a970 and image dd0026
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 61758b and image d91c84
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SC
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 68d663 and image 738c1a
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure L_Lung
pydicer.analyse.data - INFO - Computing radiomics for structure set b5bddb and image 6834c9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set cc682f and image 666be6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 8e34f9 and image 2bf2f9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
[6]:
| Contour | Patient | ImageHashedUID | StructHashedUID | ResampledPixelSpacing | NormalisationScale | firstorder|10Percentile | firstorder|90Percentile | firstorder|Energy | firstorder|Entropy | ... | shape|Maximum2DDiameterColumn | shape|Maximum2DDiameterRow | shape|Maximum2DDiameterSlice | shape|Maximum3DDiameter | shape|MeshVolume | shape|MinorAxisLength | shape|Sphericity | shape|SurfaceArea | shape|SurfaceVolumeRatio | shape|VoxelVolume | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Esophagus | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -9.0 | 74.0 | 6.379739e+06 | 2.563380 | ... | 223.924778 | 222.309084 | 23.619884 | 224.231209 | 3.193220e+04 | 50.733471 | 0.408351 | 11919.810387 | 0.373285 | 3.316495e+04 |
| 4 | Heart | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -14.0 | 68.0 | 8.486142e+07 | 2.343017 | ... | 163.733306 | 127.040344 | 151.241053 | 164.152138 | 7.510135e+05 | 100.977462 | 0.781597 | 51121.049949 | 0.068069 | 7.526486e+05 |
| 0 | Lung_L | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -871.0 | -502.0 | 3.907161e+10 | 4.313815 | ... | 236.649430 | 242.714238 | 190.429595 | 245.982024 | 1.802886e+06 | 171.702531 | 0.568696 | 125964.905979 | 0.069868 | 1.801747e+06 |
| 2 | Lung_R | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -889.0 | -480.0 | 4.790689e+10 | 4.414603 | ... | 231.159117 | 247.961931 | 186.213760 | 248.126635 | 2.159708e+06 | 172.513299 | 0.582917 | 138614.093158 | 0.064182 | 2.161386e+06 |
| 3 | SpinalCord | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | -19.0 | 70.0 | 6.830546e+06 | 2.638360 | ... | 300.128718 | 313.974459 | 26.529436 | 314.315983 | 7.050233e+04 | 32.966235 | 0.418454 | 19722.946105 | 0.279749 | 7.217496e+04 |
5 rows × 38 columns
You can also set a specific subset of features like this:
[7]:
# Specify features to compute grouped by class
compute_radiomics = {
"firstorder": ["Maximum", "Minimum", "Mean", "Median"],
"shape": ["SurfaceArea", "VoxelVolume"],
}
# Pass the dict to the compute the radiomics
pydicer.analyse.compute_radiomics(radiomics=compute_radiomics)
df_radiomics = pydicer.analyse.get_all_computed_radiomics_for_dataset()
df_radiomics.head()
pydicer.analyse.data - INFO - Computing radiomics for structure set ed6686 and image 5adf40
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set ceb111 and image 88c5ef
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 6c6ea4 and image 914d57
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set f036b8 and image aa38e6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Right
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Left
pydicer.analyse.data - INFO - Computing radiomics for structure set 48a970 and image dd0026
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 61758b and image d91c84
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SC
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 68d663 and image 738c1a
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure L_Lung
pydicer.analyse.data - INFO - Computing radiomics for structure set b5bddb and image 6834c9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set cc682f and image 666be6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 8e34f9 and image 2bf2f9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
[7]:
| Contour | Patient | ImageHashedUID | StructHashedUID | ResampledPixelSpacing | NormalisationScale | firstorder|Maximum | firstorder|Minimum | firstorder|Mean | firstorder|Median | shape|SurfaceArea | shape|VoxelVolume | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Esophagus | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 195.0 | -745.0 | 33.382764 | 42.0 | 11919.810387 | 3.316495e+04 |
| 4 | Heart | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 229.0 | -577.0 | 34.078823 | 44.0 | 51121.049949 | 7.526486e+05 |
| 0 | Lung_L | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 357.0 | -1000.0 | -729.756106 | -778.0 | 125964.905979 | 1.801747e+06 |
| 2 | Lung_R | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 215.0 | -1000.0 | -735.842185 | -789.0 | 138614.093158 | 2.161386e+06 |
| 3 | SpinalCord | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 429.0 | -144.0 | 27.051730 | 27.0 | 19722.946105 | 7.217496e+04 |
Track Metadata#
When analysing your radiomic features, it may be useful to have certain metadata available from either the image or structure set. You can specify which DICOM header tags to extract metadata for and these will be stored alongside the radiomic feature values.
In the cell below, we recompute our radiomics and store the PatientSex header value from the image series and the StudyDate value from the structure set.
[8]:
# Compute the radiomics specifying the meta data to keep
pydicer.analyse.compute_radiomics(
radiomics=compute_radiomics,
image_meta_data=["PatientSex"],
structure_meta_data=["StudyDate"]
)
# Fetch the results and display the first rows
df_radiomics = pydicer.analyse.get_all_computed_radiomics_for_dataset()
df_radiomics.head()
pydicer.analyse.data - INFO - Computing radiomics for structure set ed6686 and image 5adf40
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set ceb111 and image 88c5ef
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 6c6ea4 and image 914d57
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set f036b8 and image aa38e6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Right
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_Left
pydicer.analyse.data - INFO - Computing radiomics for structure set 48a970 and image dd0026
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 61758b and image d91c84
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SC
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 68d663 and image 738c1a
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - DEBUG - Computing radiomics for structure L_Lung
pydicer.analyse.data - INFO - Computing radiomics for structure set b5bddb and image 6834c9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set cc682f and image 666be6
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.analyse.data - INFO - Computing radiomics for structure set 8e34f9 and image 2bf2f9
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_L
pydicer.analyse.data - DEBUG - Computing radiomics for structure Esophagus
pydicer.analyse.data - DEBUG - Computing radiomics for structure Lung_R
pydicer.analyse.data - DEBUG - Computing radiomics for structure SpinalCord
pydicer.analyse.data - DEBUG - Computing radiomics for structure Heart
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
pydicer.dataset.structureset - WARNING - No mapping file found with id default
[8]:
| Contour | Patient | ImageHashedUID | StructHashedUID | ResampledPixelSpacing | NormalisationScale | firstorder|Maximum | firstorder|Minimum | firstorder|Mean | firstorder|Median | shape|SurfaceArea | shape|VoxelVolume | struct|StudyDate | img|PatientSex | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Esophagus | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 195.0 | -745.0 | 33.382764 | 42.0 | 11919.810387 | 3.316495e+04 | 20040303 | M |
| 4 | Heart | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 229.0 | -577.0 | 34.078823 | 44.0 | 51121.049949 | 7.526486e+05 | 20040303 | M |
| 0 | Lung_L | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 357.0 | -1000.0 | -729.756106 | -778.0 | 125964.905979 | 1.801747e+06 | 20040303 | M |
| 2 | Lung_R | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 215.0 | -1000.0 | -735.842185 | -789.0 | 138614.093158 | 2.161386e+06 | 20040303 | M |
| 3 | SpinalCord | LCTSC-Test-S1-101 | 666be6 | cc682f | NaN | NaN | 429.0 | -144.0 | 27.051730 | 27.0 | 19722.946105 | 7.217496e+04 | 20040303 | M |
[ ]: