libflowcam 0.1

A Python module for interacting with IFCB data.

libflowcam

An optimised, native Python library for working with FlowCam data. Implements lazy-loading wherever possible and maintains open file pointers for speedy access. Returns standard Pillow image objects for further processing.

Example

from libflowcam import ROIReader

# Represents a typical sample density
sample1 = ROIReader("testdata/flowcam_polina_pontoon_0907_r2/flowcam_polina_pontoon_0907_r2.csv")
print(str(len(sample1.rois)) + " ROIs") # Should be 6268 ROIs
for roi_index in [10, 100, 1000]:
    sample1.rois[roi_index].image.save("testout/flowcam_polina_pontoon_0907_r2_" + str(roi_index) + ".png")

# A very dense sample, this is a cruel test
sample2 = ROIReader("testdata/flowcam_polina_pontoon_0707_r1/flowcam_polina_pontoon_0707_r1.csv")
print(str(len(sample2.rois)) + " ROIs") # Should be 137015 ROIs
for roi_index in [10, 100, 1000, 10000, 100000]:
    sample2.rois[roi_index].image.save("testout/flowcam_polina_pontoon_0707_r1_" + str(roi_index) + ".png")