io3d
This package contains set of functions used for reading and writing 3D data.
Install
Use anaconda
conda install -c mjirik -c conda-forge -c SimpleITK -c bioconda io3dor
pip install io3dYou can use 3D viewer sed3 for visualization.
pip install sed3Examples
Read and show data from url
import io3d
import matplotlib.pyplot as plt
datap = io3d.read("http://home.zcu.cz/~mjirik/lisa/sample_data/nrn4.pklz")
plt.imshow(datap.data3d[10,:,:], cmap='gray')
plt.show()Get sample data
Data will be automatically downloaded to ~\data\
command line:
python -m io3d -l 3Dircadb1.1Read data and see one slice
import io3d
from matplotlib import pyplot as plt
# get path the data stored in default data directory
pth = io3d.datasets.joinp("medical/orig/3Dircadb1.1/MASKS_DICOM/")
datap = io3d.read(pth)
print(datap.voxelsize_mm)
# size of voxel can be accessed also by datap["voxelsize_mm"]
# see slice 10
plt.imshow(datap.data3d[5,:,:], cmap='gray')
plt.show()Intensity image data3d and voxelsize_mm can be accessed easier through the datap properies
Use object DataReader and see data in simple viewer
import io3d
import sed3
pth = io3d.datasets.joinp("medical/orig/3Dircadb1.1/MASKS_DICOM/")
dr = io3d.DataReader()
datap = dr.Get3DData(pth, dataplus_format=True)
ed = sed3.sed3(datap['data3d'])
ed.show()Use CLI
python io3d/datareader.py -i ./sample_data/jatra_5mm/Use it in your application - Qt Widget
import sys
from PyQt5 import QtGui
import io3d.datareaderqt
app = QtGui.QApplication(sys.argv)
w = io3d.datereaderqt.DatareaderWidget()
w.show()
app.exec_()
datap = w.datap
Dataset
Read more about dataset setup and how to use datasets.
Get sample data with io3d package:
python -m io3d -l 3Dircadb1.1Get list of available datasets:
python -m io3d -L... or download data:
Put this data into sample_data dir.
File or directory checksum
python -m io3d -c directory_pathSpecific dataset path
Some parts of dataset can be stored separately. You can set it by command
python -m io3d -ssdp "g:/Můj disk/data/biology/roots" "biology/roots"
python -m io3d -ssdp "g:/Můj disk/data/medical/orig/sliver07" "medical/orig/sliver07"or you can edit ~\.io3d_cache.yaml
Get by url
Data can be downloaded from url. Just use URL instead of label.
The local path can be specified by adding local path to the end of url separated by colon.'
python -m io3d.datasets -l http://home.zcu.cz/~mjirik/lisa/sample_data/biodur_sample.zip:biodur_sample/python -m io3d.datasets -l https://downloads.openmicroscopy.org/images/OME-TIFF/2016-06/bioformats-artificial/time-series.ome.tif:biology/orig/rootsRead datasets coherently
import io3d
import matplotlib.pyplot as plt
datap1 = io3d.read_dataset("3Dircadb1", "data3d", 1)
datap2 = io3d.read_dataset("3Dircadb1", "bone", 1)
plt.imshow(datap1["data3d"][20,:,:], cmap="gray")
plt.contour(datap2["data3d"][20,:,:])
plt.show()
Now you can read the sliver07 dataset in the same way. Just put it in data/orig/medical/sliver07
import io3d
import matplotlib.pyplot as plt
datap1 = io3d.read_dataset("sliver07", "data3d", 1)
plt.imshow(datap1["data3d"][20,:,:], cmap="gray")
plt.show()The path where the datafiles are looked for can be checked by get_dataset_path function.
import io3d.datasets
pth = io3d.datasets.get_dataset_path("sliver07", "data3d", 1)
