search

vitessce / vitessce-data

Utils for loading HuBMAP data formats
MIT License
6 stars 4 forks source link

Add IMS spraggins dataset #66

Closed manzt closed 4 years ago

manzt commented 4 years ago
mccalluc commented 4 years ago

Cool: I'll look. Travis fails on:

Traceback (most recent call last):
  File "/home/travis/build/hms-dbmi/vitessce-data/python/imzml_reader.py", line 125, in <module>
    dataset.write_zarr(args.ims_file, dtype="i4")
  File "/home/travis/build/hms-dbmi/vitessce-data/python/imzml_reader.py", line 87, in write_zarr
    arr = self.to_array()
  File "/home/travis/build/hms-dbmi/vitessce-data/python/imzml_reader.py", line 82, in to_array
    arr[:, x - x_min, y - y_min] = intensities
ValueError: could not broadcast input array from shape (0) into shape (47)
manzt commented 4 years ago

@mccalluc I added zlib compression to the zarr output and commented on some of the numpy-specific things. Let me know if you have any questions!