How to use the zarr.zeros function in zarr

To help you get started, we’ve selected a few zarr examples, based on popular ways it is used in public projects.

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github tskit-dev / tsinfer / tests / test_formats.py View on Github external
def test_mixed_chunk_sizes(self):
        source = {"a": zarr.zeros(10, chunks=(1,)), "b": zarr.zeros(10, chunks=(2,))}
        self.assertRaises(ValueError, formats.BufferedItemWriter, source)
github google / neuroglancer / python / examples / flood_filling_simulation.py View on Github external
def _do_flood_fill(self, initial_pos, inf_results, inf_volume, event):
        initial_pos = (int(initial_pos[0]), int(initial_pos[1]), int(initial_pos[2]))

        gt_vol_zarr = zarr.zeros(
            self.gt_vol.bounds.to_list()[3:], chunks=(64, 64, 64), dtype=np.uint64)

        gt_blocks_seen = set()

        block_size = np.array((64, 64, 64), np.int64)

        def fetch_gt_block(block):
            spos = block * block_size
            epos = spos + block_size
            slice_expr = np.s_[int(spos[0]):int(epos[0]),
                               int(spos[1]):int(epos[1]),
                               int(spos[2]):int(epos[2])]
            gt_data = self.gt_vol[slice_expr][..., 0]
            gt_vol_zarr[slice_expr] = gt_data

        def get_patch(spos, epos):
github google / neuroglancer / python / examples / flood_filling_simulation.py View on Github external
def _start_flood_fill(self, pos):
        self._stop_flood_fill()
        inf_results = zarr.zeros(
            self.gt_vol.bounds.to_list()[3:], chunks=(64, 64, 64), dtype=np.uint8)
        inf_volume = neuroglancer.LocalVolume(
            data=inf_results, dimensions=self.dimensions)

        with self.viewer.txn() as s:
            s.layers['points'] = neuroglancer.LocalAnnotationLayer(self.dimensions)
            s.layers['inference'] = neuroglancer.ImageLayer(
                source=inf_volume,
                shader='''
void main() {
  float v = toNormalized(getDataValue(0));
  vec4 rgba = vec4(0,0,0,0);
  if (v != 0.0) {
    rgba = vec4(colormapJet(v), 1.0);
  }
  emitRGBA(rgba);
github napari / napari / examples / zarr_nD_image.py View on Github external
"""
Display a zarr array
"""

try:
    import zarr
except ImportError:
    raise ImportError("""This example uses a zarr array but zarr is not
    installed. To install try 'pip install zarr'.""")

import napari


with napari.gui_qt():
    data = zarr.zeros((102_0, 200, 210), chunks=(100, 200, 210))
    data[53_0:53_1, 100:110, 110:120] = 1

    print(data.shape)
    # For big data, we should specify the contrast_limits range, or napari will try
    # to find the min and max of the full image.
    viewer = napari.view_image(data, contrast_limits=[0, 1], rgb=False)
github google / neuroglancer / python / examples / interactive_inference.py View on Github external
def __init__(self):
        viewer = self.viewer = neuroglancer.Viewer()
        viewer.actions.add('inference', self._do_inference)
        self.gt_vol = cloudvolume.CloudVolume(
            'https://storage.googleapis.com/neuroglancer-public-data/flyem_fib-25/ground_truth',
            mip=0,
            bounded=True,
            progress=False,
            provenance={})
        self.dimensions = neuroglancer.CoordinateSpace(
            names=['x', 'y', 'z'],
            units='nm',
            scales=self.gt_vol.resolution,
        )
        self.inf_results = zarr.zeros(
            self.gt_vol.bounds.to_list()[3:], chunks=(64, 64, 64), dtype=np.uint8)
        self.inf_volume = neuroglancer.LocalVolume(
            data=self.inf_results, dimensions=self.dimensions)
        with viewer.config_state.txn() as s:
            s.input_event_bindings.data_view['shift+mousedown0'] = 'inference'

        with viewer.txn() as s:
            s.layers['image'] = neuroglancer.ImageLayer(
                source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
            )
            s.layers['ground_truth'] = neuroglancer.SegmentationLayer(
                source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth',
            )
            s.layers['ground_truth'].visible = False
            s.layers['inference'] = neuroglancer.ImageLayer(
                source=self.inf_volume,