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[WIP] updates for napari 0.2.0 release #1591

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[WIP] updates for napari 0.2.0 release #1591

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17 changes: 7 additions & 10 deletions starfish/core/_display.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
Viewer = None


NAPARI_VERSION = "0.1.5" # when changing this, update docs in display
NAPARI_VERSION = "0.2.0" # when changing this, update docs in display
INTERACTIVE = not hasattr(__main__, "__file__")


Expand Down Expand Up @@ -109,10 +109,6 @@ def _spots_to_markers(intensity_table: IntensityTable) -> Tuple[np.ndarray, np.n
coords[:, 4] = np.repeat(intensity_table[Features.AXIS][Axes.X.value].values, code_length)

sizes = np.repeat(intensity_table.radius.values, code_length)
rc = np.zeros((sizes.shape[0], 2), dtype=int)
z = sizes[:, np.newaxis]
yx = np.tile(sizes[:, np.newaxis], (1, 2))
sizes = np.concatenate((rc, yx, z), axis=1)

return coords, sizes

Expand Down Expand Up @@ -198,7 +194,7 @@ def display(
- To use in ipython, use the `%gui qt` magic.
- napari axes currently cannot be labeled. Until such a time that they can, this function will
order them by Round, Channel, and Z.
- Requires at least napari 0.1.5: use `pip install starfish[napari]`
- Requires at least napari 0.2.0: use `pip install starfish[napari]`
to install all necessary requirements
"""
if stack is None and spots is None and masks is None:
Expand Down Expand Up @@ -238,7 +234,7 @@ def display(
stack = stack.max_proj(*project_axes)

viewer.add_image(stack.xarray.values,
multichannel=False,
rgb=False,
name="stack")

if spots is not None:
Expand All @@ -260,15 +256,16 @@ def display(
coords = coords[mask]
sizes = sizes[mask]

# adjust z-size
sizes[:, 4] *= z_multiplier
# Set anisotropy factor for data orderd r, c, z, y, x.
anisotropy = np.multiply((0, 0, z_multiplier, 1, 1), radius_multiplier)

viewer.add_points(
coords,
face_color="red",
edge_color="red",
symbol="ring",
size=sizes * radius_multiplier,
size=sizes,
anisotropy=anisotropy,
n_dimensional=True,
name="spots"
)
Expand Down