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 io3d

or

pip install io3d

You can use 3D viewer sed3 for visualization.

pip install sed3

Examples

Check the tutorial

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 3Dircadb1.1

Read 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 3Dircadb1.1

Get list of available datasets:

python -m io3d -L

... or download data:

io3d_sample_data

ct_head.rawiv

Put this data into sample_data dir.

File or directory checksum

python -m io3d -c directory_path

Specific 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/roots

Read 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)