Dataset Inventory¶

In the first tutorial we will show how to search for available data using the hoa_tools.inventory module. By the end you should know how to search and filter the built in dataset inventory.

In [1]:

import pandas as pd

import pandas as pd

In [2]:

import hoa_tools.inventory

import hoa_tools.inventory

In [3]:

pd.options.display.width = None  # type: ignore[assignment]

pd.options.display.width = None # type: ignore[assignment]

Loading the inventory¶

First we'll load the inventory::

In [4]:

inventory = hoa_tools.inventory.load_inventory()
inventory

inventory = hoa_tools.inventory.load_inventory() inventory

Out[4]:

	donor	organ	organ_context	voi	voxel_size_um
S-20-28_kidney_VOI-02_6.51um_bm05	S-20-28	kidney	NaN	VOI-02	6.510
LADAF-2020-27_liver_complete-organ_19.61um_bm18	LADAF-2020-27	liver	NaN	complete-organ	19.610
S-21-46_brain_complete-organ_19.57um_bm18	S-21-46	brain	NaN	complete-organ	19.570
FO-20-135_lung_complete-organ_25.25um_bm05	FO-20-135	lung	NaN	complete-organ	25.250
LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_6.5um_bm05	LADAF-2020-27	lung	left	VOI-01-upper-lobe-apical	6.500
...	...	...	...	...	...
LADAF-2021-64_heart_VOI-04_6.51um_bm18	LADAF-2021-64	heart	NaN	VOI-04	6.510
FO-20-155_lung_col4_6.5um_bm05	FO-20-155	lung	NaN	col4	6.500
LADAF-2021-17_brain_complete-organ_42.4um_bm18	LADAF-2021-17	brain	NaN	complete-organ	42.400
S-20-29_heart_VOI-02_6.51um_bm18	S-20-29	heart	NaN	VOI-02	6.510
LADAF-2021-17_heart_ROI-7.1_2.256um_bm18	LADAF-2021-17	heart	NaN	ROI-7.1	2.256

378 rows × 5 columns

The inventory is a pandas.DataFrame object. Each row is a different dataset, and each column contains the properties of the dataset. The available columns are::

In [5]:

print(list(inventory.columns))

print(list(inventory.columns))

['donor', 'organ', 'organ_context', 'voi', 'voxel_size_um']

Searching the inventory¶

To find all the spleen datasets we can filter the dataframe::

In [6]:

inventory[inventory["organ"] == "spleen"]

inventory[inventory["organ"] == "spleen"]

Out[6]:

	donor	organ	organ_context	voi	voxel_size_um
LADAF-2022-16_spleen_complete-organ_15.75um_bm18	LADAF-2022-16	spleen	NaN	complete-organ	15.75
LADAF-2020-27_spleen_central-column_1.29um_bm05	LADAF-2020-27	spleen	NaN	central-column	1.29
LADAF-2020-27_spleen_complete-organ_25.08um_bm05	LADAF-2020-27	spleen	NaN	complete-organ	25.08
LADAF-2021-17_spleen_complete-organ_25.0um_bm05	LADAF-2021-17	spleen	NaN	complete-organ	25.00
LADAF-2020-27_spleen_central-column_6.05um_bm05	LADAF-2020-27	spleen	NaN	central-column	6.05