Neurosift shows images rotated

[h-mayorquin]

But in neurosift:

Code to reproduce

import numpy as np 
img  = np.zeros((1000,1000))
img[:, 200:400] = 1

plt.imshow(img, cmap="gray")
# plt.imshow(np.rot90(img, k=1), cmap="gray")

from pynwb.testing.mock.file import mock_NWBFile
from pynwb.image import GrayscaleImage, Images

nwbfile = mock_NWBFile()

image = GrayscaleImage(name='test_image', data=img)

images_container = Images(
    name="stimuli",
    images=[image],
    description=f"test image",
)

nwbfile.add_stimulus(images_container)

from pynwb import NWBHDF5IO

with NWBHDF5IO('test.nwb', 'w') as io:
    io.write(nwbfile)
    
with NWBHDF5IO('test.nwb', 'r') as io:
    nwbfile_read = io.read()
    image_data = nwbfile_read.stimulus["stimuli"].images["test_image"].data
    plt.imshow(image_data, cmap="gray")

[magland]

Thanks @h-mayorquin for the very helpful example for calibration. I have fixed this.

@CodyCBakerPhD @bendichter This change is going to affect the Neurosift orientation of all Image neurodata objects. I know there was discussion about having a rotate button in NS, but in this case (where it's an "Image") I feel like there should be one true orientation, so if it works with @h-mayorquin 's example, then we should be good? I could be wrong about this though, that's why I'm tagging you.

BTW, a slightly updated script that adds a bit more structure to calibrate the vertical flip

import numpy as np
import matplotlib.pyplot as plt
from pynwb.testing.mock.file import mock_NWBFile
from pynwb.image import GrayscaleImage, Images
from pynwb import NWBHDF5IO


img = np.zeros((1000, 1500))
img[:, 200:400] = 1
img[0:50][:, 200:400] = 0.5

plt.imshow(img, cmap="gray")
# plt.imshow(np.rot90(img, k=1), cmap="gray")

nwbfile = mock_NWBFile()

image = GrayscaleImage(name="test_image", data=img)

images_container = Images(
    name="stimuli",
    images=[image],
    description=f"test image",
)

nwbfile.add_stimulus(images_container)

with NWBHDF5IO("test.nwb", "w") as io:
    io.write(nwbfile)

with NWBHDF5IO("test.nwb", "r") as io:
    nwbfile_read = io.read()
    image_data = nwbfile_read.stimulus["stimuli"].images["test_image"].data
    plt.imshow(image_data, cmap="gray")

plt.show()

Then compare that plot with

neurosift view-nwb test.nwb

[h-mayorquin]

Thanks a bunch!

This works for my current dataset: