Refactor of labels logic#336

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Merged
timtreis merged 4 commits into from
Aug 29, 2024
Merged

Refactor of labels logic #336

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0c28304
enabled edgecase; refactor
timtreis Aug 28, 2024
6cc7c06
added test
timtreis Aug 28, 2024
7b80197
Reverted behaviour, was correct
timtreis Aug 28, 2024
86ecc44
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 28, 2024
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121 changes: 27 additions & 94 deletions src/spatialdata_plot/pl/render.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
stacked = np.stack([layers[c] for c in channels], axis=-1)
else: # -> use given cmap for each channel
channel_cmaps = [render_params.cmap_params.cmap] * n_channels
# Apply cmaps to each channel, add up and normalize to [0, 1]
stacked = (
np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
)
# Remove alpha channel so we can overwrite it from render_params.alpha
stacked = stacked[:, :, :3]
logger.warning(
"One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

# Apply cmaps to each channel and add up
colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

# Remove alpha channel so we can overwrite it from render_params.alpha
colored = colored[:, :, :3]

_ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
raise ValueError("If 'palette' is provided, its length must match the number of channels.")

channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

# Apply cmaps to each channel and add up
colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

# Remove alpha channel so we can overwrite it from render_params.alpha
colored = colored[:, :, :3]

_ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

elif palette is None and got_multiple_cmaps:
channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

# Apply cmaps to each channel, add up and normalize to [0, 1]
colored = (
np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
)

# Remove alpha channel so we can overwrite it from render_params.alpha
colored = colored[:, :, :3]

_ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
table_name=table_name,
)

# default case: no contour, just fill
# if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
labels_infill = _map_color_seg(
def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
labels = _map_color_seg(
seg=label.values,
cell_id=instance_id,
color_vector=color_vector,
color_source_vector=color_source_vector,
cmap_params=render_params.cmap_params,
seg_erosionpx=None,
seg_boundaries=False,
seg_erosionpx=seg_erosionpx,
seg_boundaries=seg_boundaries,
na_color=render_params.cmap_params.na_color,
na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
)

_cax = ax.imshow(
labels_infill,
labels,
rasterized=True,
cmap=None if categorical else render_params.cmap_params.cmap,
norm=None if categorical else render_params.cmap_params.norm,
alpha=render_params.fill_alpha,
alpha=alpha,
origin="lower",
zorder=render_params.zorder,
)
_cax.set_transform(trans_data)
cax = ax.add_image(_cax)
return cax # noqa: RET504

# default case: no contour, just fill
# since contour_px is passed to skimage.morphology.erosion to create the contour,
# any border thickness is only within the label, not outside. Therefore, the case
# of fill_alpha == outline_alpha is equivalent to fill-only
if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
render_params.fill_alpha == render_params.outline_alpha
):
cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
alpha_to_decorate_ax = render_params.fill_alpha

# outline-only case
if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
labels_contour = _map_color_seg(
seg=label.values,
cell_id=instance_id,
color_vector=color_vector,
color_source_vector=color_source_vector,
cmap_params=render_params.cmap_params,
seg_erosionpx=render_params.contour_px,
seg_boundaries=True,
na_color=render_params.cmap_params.na_color,
na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
cax = _draw_labels(
seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
)
_cax = ax.imshow(
labels_contour,
rasterized=True,
cmap=None if categorical else render_params.cmap_params.cmap,
norm=None if categorical else render_params.cmap_params.norm,
alpha=render_params.outline_alpha,
origin="lower",
zorder=render_params.zorder,
)
_cax.set_transform(trans_data)
cax = ax.add_image(_cax)
alpha_to_decorate_ax = render_params.outline_alpha

# pretty case: both outline and infill
if (
render_params.fill_alpha > 0.0
and render_params.outline_alpha > 0.0
and render_params.fill_alpha != render_params.outline_alpha
):
elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
# first plot the infill ...
label_infill = _map_color_seg(
seg=label.values,
cell_id=instance_id,
color_vector=color_vector,
color_source_vector=color_source_vector,
cmap_params=render_params.cmap_params,
seg_erosionpx=None,
seg_boundaries=False,
na_color=render_params.cmap_params.na_color,
na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
)

_cax_infill = ax.imshow(
label_infill,
rasterized=True,
cmap=None if categorical else render_params.cmap_params.cmap,
norm=None if categorical else render_params.cmap_params.norm,
alpha=render_params.fill_alpha,
origin="lower",
zorder=render_params.zorder,
)
_cax_infill.set_transform(trans_data)
cax_infill = ax.add_image(_cax_infill)
cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

# ... then overlay the contour
label_contour = _map_color_seg(
seg=label.values,
cell_id=instance_id,
color_vector=color_vector,
color_source_vector=color_source_vector,
cmap_params=render_params.cmap_params,
seg_erosionpx=render_params.contour_px,
seg_boundaries=True,
na_color=render_params.cmap_params.na_color,
na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
cax_contour = _draw_labels(
seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
)

_cax_contour = ax.imshow(
label_contour,
rasterized=True,
cmap=None if categorical else render_params.cmap_params.cmap,
norm=None if categorical else render_params.cmap_params.norm,
alpha=render_params.outline_alpha,
origin="lower",
zorder=render_params.zorder,
)
_cax_contour.set_transform(trans_data)
cax_contour = ax.add_image(_cax_contour)

# pass the less-transparent _cax for the legend
cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

else:
raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

_ = _decorate_axs(
ax=ax,
cax=cax,
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Refactor of labels logic#336

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 Merged

timtreis
merged 4 commits into

from

Aug 29, 2024
 Merged


Refactor of labels logic
#336
 Changes from all commits
Commits

Show all changes


4 commits


Select commit
Hold shift + click to select a range
0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Refactor of labels logic#336

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 Merged

timtreis
merged 4 commits into

from

Aug 29, 2024
 Merged


Refactor of labels logic
#336
 Changes from all commits
Commits

Show all changes


4 commits


Select commit
Hold shift + click to select a range
0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

File filter

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Refactor of labels logic#336

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 Merged

timtreis
merged 4 commits into

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Aug 29, 2024
 Merged


Refactor of labels logic
#336
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0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Refactor of labels logic#336

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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to your account

 Merged

timtreis
merged 4 commits into

from

Aug 29, 2024
 Merged


Refactor of labels logic
#336
 Changes from all commits
Commits

Show all changes


4 commits


Select commit
Hold shift + click to select a range
0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

File filter

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Filter by extension
Conversations

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Refactor of labels logic#336

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 Merged

timtreis
merged 4 commits into

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Aug 29, 2024
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Refactor of labels logic
#336
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0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Refactor of labels logic#336

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 Merged

timtreis
merged 4 commits into

from

Aug 29, 2024
 Merged


Refactor of labels logic
#336
 Changes from all commits
Commits

Show all changes


4 commits


Select commit
Hold shift + click to select a range
0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Refactor of labels logic#336

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 Merged

timtreis
merged 4 commits into

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Aug 29, 2024
 Merged


Refactor of labels logic
#336
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0c28304

enabled edgecase; refactor


timtreis Aug 28, 2024
6cc7c06

added test


timtreis Aug 28, 2024
7b80197

Reverted behaviour, was correct


timtreis Aug 28, 2024
86ecc44

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Aug 28, 2024

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121 changes: 27 additions & 94 deletions
src/spatialdata_plot/pl/render.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -650,11 +650,9 @@ def _render_images(
 stacked = np.stack([layers[c] for c in channels], axis=-1)
 else: # -> use given cmap for each channel
 channel_cmaps = [render_params.cmap_params.cmap] * n_channels
 # Apply cmaps to each channel, add up and normalize to [0, 1]
 stacked = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )
 # Remove alpha channel so we can overwrite it from render_params.alpha
 stacked = stacked[:, :, :3]
 logger.warning(
 "One cmap was given for multiple channels and is now used for each channel. "
Expand All@@ -676,11 +674,7 @@ def _render_images(
 seed_colors = _get_colors_for_categorical_obs(list(range(n_channels)))

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in seed_colors]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand All@@ -691,24 +685,16 @@ def _render_images(
 raise ValueError("If 'palette' is provided, its length must match the number of channels.")

 channel_cmaps = [_get_linear_colormap([c], "k")[0] for c in palette if isinstance(c, str)]

 # Apply cmaps to each channel and add up
 colored = np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0)

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)

 elif palette is None and got_multiple_cmaps:
 channel_cmaps = [cp.cmap for cp in render_params.cmap_params] # type: ignore[union-attr]

 # Apply cmaps to each channel, add up and normalize to [0, 1]
 colored = (
 np.stack([channel_cmaps[ind](layers[ch]) for ind, ch in enumerate(channels)], 0).sum(0) / n_channels
 )

 # Remove alpha channel so we can overwrite it from render_params.alpha
 colored = colored[:, :, :3]

 _ax_show_and_transform(colored, trans_data, ax, render_params.alpha, zorder=render_params.zorder)
Expand DownExpand Up@@ -794,119 +780,66 @@ def _render_labels(
 table_name=table_name,
 )

 # default case: no contour, just fill
 # if fill_alpha and outline_alpha are the same, we're technically also at a no-outline situation
 if render_params.outline_alpha == 0.0 or render_params.outline_alpha == render_params.fill_alpha:
 labels_infill = _map_color_seg(
 def _draw_labels(seg_erosionpx: int | None, seg_boundaries: bool, alpha: float) -> matplotlib.image.AxesImage:
 labels = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 seg_erosionpx=seg_erosionpx,
 seg_boundaries=seg_boundaries,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax = ax.imshow(
labels_infill,
labels,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 alpha=alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 return cax # noqa: RET504

 # default case: no contour, just fill
 # since contour_px is passed to skimage.morphology.erosion to create the contour,
 # any border thickness is only within the label, not outside. Therefore, the case
 # of fill_alpha == outline_alpha is equivalent to fill-only
 if (render_params.fill_alpha > 0.0 and render_params.outline_alpha == 0.0) or (
 render_params.fill_alpha == render_params.outline_alpha
 ):
 cax = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)
 alpha_to_decorate_ax = render_params.fill_alpha

 # outline-only case
 if render_params.fill_alpha == 0.0 and render_params.outline_alpha != 0.0:
 labels_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 elif render_params.fill_alpha == 0.0 and render_params.outline_alpha > 0.0:
 cax = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )
 _cax = ax.imshow(
 labels_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 alpha_to_decorate_ax = render_params.outline_alpha

 # pretty case: both outline and infill
 if (
 render_params.fill_alpha > 0.0
 and render_params.outline_alpha > 0.0
 and render_params.fill_alpha != render_params.outline_alpha
 ):
 elif render_params.fill_alpha > 0.0 and render_params.outline_alpha > 0.0:
 # first plot the infill ...
 label_infill = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=None,
 seg_boundaries=False,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 )

 _cax_infill = ax.imshow(
 label_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_infill.set_transform(trans_data)
 cax_infill = ax.add_image(_cax_infill)
 cax_infill = _draw_labels(seg_erosionpx=None, seg_boundaries=False, alpha=render_params.fill_alpha)

 # ... then overlay the contour
 label_contour = _map_color_seg(
 seg=label.values,
 cell_id=instance_id,
 color_vector=color_vector,
 color_source_vector=color_source_vector,
 cmap_params=render_params.cmap_params,
 seg_erosionpx=render_params.contour_px,
 seg_boundaries=True,
 na_color=render_params.cmap_params.na_color,
 na_color_modified_by_user=render_params.cmap_params.na_color_modified_by_user,
 cax_contour = _draw_labels(
 seg_erosionpx=render_params.contour_px, seg_boundaries=True, alpha=render_params.outline_alpha
 )

 _cax_contour = ax.imshow(
 label_contour,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.outline_alpha,
 origin="lower",
 zorder=render_params.zorder,
 )
 _cax_contour.set_transform(trans_data)
 cax_contour = ax.add_image(_cax_contour)

 # pass the less-transparent _cax for the legend
 cax = cax_infill if render_params.fill_alpha > render_params.outline_alpha else cax_contour
 alpha_to_decorate_ax = max(render_params.fill_alpha, render_params.outline_alpha)

 else:
 raise ValueError("Parameters 'fill_alpha' and 'outline_alpha' cannot both be 0.")

 _ = _decorate_axs(
 ax=ax,
 cax=cax,
Expand Down