Helper Module for Deep Learning.

Module that provides functions to prepare the TCGA-LGG-tif dataset.

class pynet.datasets.tcga_lgg_tif.Item(input_path, output_path, metadata_path, height, width)¶

property height¶

Alias for field number 3

property input_path¶

Alias for field number 0

property metadata_path¶

Alias for field number 2

property output_path¶

Alias for field number 1

property width¶

Alias for field number 4

pynet.datasets.tcga_lgg_tif.fetch_tcga_lgg_tif(datasetdir)[source]¶

Fetch/prepare the TCA-LGG-tif dataset for pynet.

The patient average age was 47 with an almost even split between women and men (56 vs. 53, 1 unknown) in our dataset. Histologically, the tumors were divided between oligodendroglioma (47), astrocytoma (33), and oligoastrocytoma (29). Histology of one tumor was unknown. The data included grade II (51) and grade III (58) tumors with grade of one tumor unknown.

Parameters

datasetdir: str

the dataset destination folder.

Returns

item: namedtuple

a named tuple containing ‘input_path’, ‘output_path’, ‘metadata_path’, ‘height’ and ‘width’.

pynet.datasets.tcga_lgg_tif.get_slice_id(fp)[source]¶

pynet.datasets.tcga_lgg_tif.get_subjects_files(datadir)[source]¶

pynet.datasets.tcga_lgg_tif.read_metadata(metadata_file)[source]¶