diff --git a/qim3d/css/gradio.css b/qim3d/css/gradio.css
index cbcb64ca98126550d8478c5cbfc5bb1e70eb7677..cbf54db560406558038f7c0f640391c90d0ef835 100644
--- a/qim3d/css/gradio.css
+++ b/qim3d/css/gradio.css
@@ -51,7 +51,7 @@ footer {
/* Input */
input[type="number" i] {
- width: 36px !important;
+ width: 64px !important;
}
input::-webkit-outer-spin-button,
@@ -235,6 +235,10 @@ div.svelte-1frtwj3 {
box-shadow: none !important;
}
+.matplotlib > img{
+ border-radius: 0.375rem !important;
+}
+
/* Hide icons from outputs */
.icon.svelte-1u5vjgs {
visibility: hidden !important;
diff --git a/qim3d/gui/local_thickness.py b/qim3d/gui/local_thickness.py
index 39fcfbb033ec710de044d26f7be12e74d134aff0..be8cfb39e7df994d12ef1462ea7d3a838a1d6750 100644
--- a/qim3d/gui/local_thickness.py
+++ b/qim3d/gui/local_thickness.py
@@ -60,17 +60,17 @@ class Interface:
session.lt_scale = args[1]
session.threshold = args[2]
session.dark_objects = args[3]
- session.flip_z = args[4]
- session.nbins = args[5]
- session.display_size_input = args[6]
- session.surface_count_input = args[7]
- session.display_size_output = args[8]
- session.surface_count_output = args[9]
- session.reversescale = args[10]
- session.show_caps = args[11]
+ session.nbins = args[4]
+ session.zpos = args[5]
+ session.cmap_originals = args[6]
+ session.cmap_lt = args[7]
return session
+ def update_session_zpos(self, session, zpos):
+ session.zpos = zpos
+ return session
+
def launch(self, **kwargs):
# Show header
if self.show_header:
@@ -107,14 +107,15 @@ class Interface:
with gr.Tab("Examples"):
gr.Examples(examples=self.img_examples, inputs=data)
- # Run button
with gr.Row():
- with gr.Column(scale=3, min_width=64):
- btn = gr.Button(
- "Run local thickness", elem_classes="btn btn-run"
- )
- with gr.Column(scale=1, min_width=64):
- btn_clear = gr.Button("Clear", elem_classes="btn btn-clear")
+ zpos = gr.Slider(
+ minimum=0,
+ maximum=1,
+ value=0.5,
+ step=0.01,
+ label="Z position",
+ info="Local thickness is calculated in 3D, this slider controls the visualization only.",
+ )
with gr.Tab("Parameters"):
gr.Markdown(
@@ -134,102 +135,87 @@ class Interface:
info="Local thickness uses a binary image, so a threshold value is needed.",
)
- dark_objects = gr.Checkbox(value=False, label="Dark objects")
-
- with gr.Tab("Display"):
- with gr.Row():
- gr.Markdown("Input display")
-
- display_size_input = gr.Slider(
- 16,
- 64,
- step=4,
- label="Display resolution",
- info="Number of voxels for the largest dimension",
- value=32,
- )
-
- surface_count_input = gr.Slider(
- 2, 16, step=1, label="Total iso-surfaces", value=4
- )
- with gr.Row():
- gr.Markdown("Output display")
-
- display_size_output = gr.Slider(
- 32,
- 128,
- step=4,
- label="Display resolution",
- info="Number of voxels for the largest dimension",
- value=64,
- )
-
- surface_count_output = gr.Slider(
- 2, 16, step=1, label="Total iso-surfaces", value=12
- )
-
- reversescale = gr.Checkbox(
- value=False, label="Reverse color scale"
+ dark_objects = gr.Checkbox(
+ value=False,
+ label="Dark objects",
+ info="Inverts the image before trhesholding. Use in case your foreground is darker than the background.",
)
- show_caps = gr.Checkbox(value=True, label="Show surface caps")
-
- flip_z = gr.Checkbox(value=True, label="Flip Z axis")
+ with gr.Tab("Display options"):
+ cmap_original = gr.Dropdown(
+ value="viridis",
+ choices=plt.colormaps(),
+ label="Colormap",
+ interactive=True,
+ )
+ cmap_lt = gr.Dropdown(
+ value="magma",
+ choices=plt.colormaps(),
+ label="Colormap",
+ interactive=True,
+ )
gr.Markdown("Thickness histogram options")
nbins = gr.Slider(
5, 50, value=25, step=1, label="Histogram bins"
)
+ # Run button
+ with gr.Row():
+ with gr.Column(scale=3, min_width=64):
+ btn = gr.Button(
+ "Run local thickness", elem_classes="btn btn-run"
+ )
+ with gr.Column(scale=1, min_width=64):
+ btn_clear = gr.Button("Clear", elem_classes="btn btn-clear")
+
inputs = [
data,
lt_scale,
threshold,
dark_objects,
- flip_z,
nbins,
- display_size_input,
- surface_count_input,
- display_size_output,
- surface_count_output,
- reversescale,
- show_caps,
+ zpos,
+ cmap_original,
+ cmap_lt,
]
with gr.Column(scale=4):
with gr.Row():
- with gr.Column(min_width=256):
- input_vol = gr.Plot(
- show_label=True, label="Original volume", visible=True
- )
+ input_vol = gr.Plot(
+ show_label=True,
+ label="Original",
+ visible=True,
+ elem_classes="plot",
+ )
- with gr.Column(min_width=256):
- binary_vol = gr.Plot(
- show_label=True, label="Binary volume", visible=True
- )
+ binary_vol = gr.Plot(
+ show_label=True,
+ label="Binary",
+ visible=True,
+ elem_classes="plot",
+ )
+ output_vol = gr.Plot(
+ show_label=True,
+ label="Local thickness",
+ visible=True,
+ elem_classes="plot",
+ )
with gr.Row():
- with gr.Column(min_width=256):
- output_vol = gr.Plot(
- show_label=True,
- label="Local thickness volume",
- visible=True,
- )
- with gr.Column(min_width=256):
- histogram = gr.Plot(
- show_label=True,
- label="Thickness histogram",
- visible=True,
- )
+ histogram = gr.Plot(
+ show_label=True,
+ label="Thickness histogram",
+ visible=True,
+ )
with gr.Row():
- with gr.Column():
- lt_output = gr.File(
- interactive=False,
- show_label=True,
- label="Output file",
- visible=False,
- elem_classes="w-320",
- )
+ lt_output = gr.File(
+ interactive=False,
+ show_label=True,
+ label="Output file",
+ visible=False,
+ elem_classes="",
+ )
# Pipelines
pipeline = Pipeline()
@@ -250,17 +236,21 @@ class Interface:
btn.click(
fn=self.start_session, inputs=inputs, outputs=session).success(
fn=pipeline.process_input, inputs=session, outputs=session).success(
- fn=pipeline.prepare_volume, inputs=session,outputs=session).success(
fn=pipeline.input_viz, inputs=session, outputs=input_vol).success(
fn=pipeline.make_binary, inputs=session, outputs=session).success(
fn=pipeline.binary_viz, inputs=session, outputs=binary_vol).success(
fn=pipeline.compute_localthickness, inputs=session, outputs=session).success(
- fn=pipeline.prepare_output_for_display, inputs=session, outputs=session).success(
fn=pipeline.output_viz, inputs=session, outputs=output_vol).success(
fn=pipeline.thickness_histogram, inputs=session, outputs=histogram).success(
fn=pipeline.save_lt, inputs=session, outputs=lt_output).success(
fn=self.make_visible, inputs=None, outputs=lt_output)
+
+ zpos.change(
+ fn=self.update_session_zpos, inputs=[session, zpos], outputs=session, show_progress=False).success(
+ fn=pipeline.input_viz, inputs=session, outputs=input_vol, show_progress=False).success(
+ fn=pipeline.binary_viz, inputs=session, outputs=binary_vol,show_progress=False).success(
+ fn=pipeline.output_viz, inputs=session, outputs=output_vol,show_progress=False)
# fmt: on
return gradio_interface
@@ -275,53 +265,24 @@ class Session:
# Args from gradio
self.data = None
- self.vol = None
self.lt_scale = None
self.threshold = 0.5
self.dark_objects = False
self.flip_z = True
self.nbins = 25
- self.display_size_input = 32
- self.surface_count_input = 4
- self.display_size_output = 64
- self.surface_count_output = 12
self.reversescale = False
- self.show_caps = True
# From pipeline
- self.vol_input_display = None
- self.input_display_size_z = None
- self.input_display_size_y = None
- self.input_display_size_x = None
- self.Zgrid = None
- self.Ygrid = None
- self.Xgrid = None
+ self.vol = None
self.vol_binary = None
- self.vol_binary_display = None
self.vol_thickness = None
- self.output_display_size_z = None
- self.output_display_size_y = None
- self.output_display_size_x = None
- self.Zgrid_output = None
- self.Ygrid_output = None
- self.Xgrid_output = None
-
- def get_vol_info(self):
- self.original_shape = np.shape(self.vol)
- self.original_Z = self.original_shape[0]
- self.original_Y = self.original_shape[1]
- self.original_X = self.original_shape[2]
- self.max_size = np.max(self.original_shape)
-
- if self.verbose:
- log.info(f"Original volume shape:{self.original_shape}")
- log.info(f"Original Z: {self.original_Z}")
- log.info(f"Original Y: {self.original_Y}")
- log.info(f"Original X: {self.original_X}")
- log.info(f"Max size: {self.max_size}")
+ self.zpos = 0
class Pipeline:
+ def __init__(self):
+ self.figsize = 6
+
def process_input(self, session):
# Load volume
session.vol = DataLoader().load(session.data.name)
@@ -334,68 +295,22 @@ class Pipeline:
return session
- def prepare_volume(self, session):
- # Get volume shape
- session.get_vol_info()
-
- # Resize for display
- session.vol_input_display = ndimage.zoom(
- input=session.vol,
- zoom=(session.display_size_input / session.max_size),
- prefilter=False,
- order=0,
- )
+ def show_slice(self, vol, z_idx, cmap="viridis"):
+ plt.close()
+ fig, ax = plt.subplots(figsize=(self.figsize, self.figsize))
- display_shape = np.shape(session.vol_input_display)
- session.input_display_size_z = display_shape[0]
- session.input_display_size_y = display_shape[1]
- session.input_display_size_x = display_shape[2]
+ ax.imshow(vol[z_idx], interpolation="nearest", cmap=cmap)
- # Create 3D grid
- session.Zgrid, session.Ygrid, session.Xgrid = np.mgrid[
- 0 : session.input_display_size_z,
- 0 : session.input_display_size_y,
- 0 : session.input_display_size_x,
- ]
+ # Adjustments
+ ax.axis("off")
+ fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
- return session
+ return fig
def input_viz(self, session):
# Generate input visualization
- data = go.Volume(
- z=session.Zgrid.flatten(),
- y=session.Ygrid.flatten(),
- x=session.Xgrid.flatten(),
- value=session.vol_input_display.flatten(),
- opacity=0.3,
- isomin=0.05 * np.max(session.vol_input_display),
- isomax=1.0 * np.max(session.vol_input_display),
- cmin=np.min(session.vol_input_display),
- cmax=np.max(session.vol_input_display),
- opacityscale="uniform",
- surface_count=session.surface_count_input,
- caps=dict(
- x_show=session.show_caps,
- y_show=session.show_caps,
- z_show=session.show_caps,
- ),
- showscale=False,
- reversescale=session.reversescale,
- )
-
- fig = go.Figure(data)
- fig.update_layout(
- scene_aspectmode="data",
- scene_xaxis_showticklabels=session.show_ticks,
- scene_yaxis_showticklabels=session.show_ticks,
- scene_zaxis_showticklabels=session.show_ticks,
- scene_xaxis_visible=session.show_axis,
- scene_yaxis_visible=session.show_axis,
- scene_zaxis_visible=session.show_axis,
- hovermode=False,
- scene_camera_eye=dict(x=1.5, y=-1.5, z=1.2),
- )
-
+ z_idx = int(session.zpos * session.vol.shape[0])
+ fig = self.show_slice(vol=session.vol, z_idx=z_idx, cmap=session.cmap_originals)
return fig
def make_binary(self, session):
@@ -403,52 +318,14 @@ class Pipeline:
# Nothing fancy, but we could add new features here
session.vol_binary = session.vol > (session.threshold * np.max(session.vol))
- session.vol_binary_display = ndimage.zoom(
- input=session.vol_binary * 255,
- zoom=(session.display_size_input / session.max_size),
- prefilter=False,
- order=0,
- )
-
return session
def binary_viz(self, session):
# Generate input visualization
- data = go.Volume(
- z=session.Zgrid.flatten(),
- y=session.Ygrid.flatten(),
- x=session.Xgrid.flatten(),
- value=session.vol_binary_display.flatten(),
- opacity=0.3,
- isomin=0.99 * np.max(session.vol_binary_display),
- isomax=1.0 * np.max(session.vol_binary_display),
- cmin=np.min(session.vol_binary_display),
- cmax=np.max(session.vol_binary_display),
- opacityscale="max",
- surface_count=2,
- caps=dict(
- x_show=session.show_caps,
- y_show=session.show_caps,
- z_show=session.show_caps,
- ),
- showscale=False,
- reversescale=session.reversescale,
- colorscale="Greys",
- )
-
- fig = go.Figure(data)
- fig.update_layout(
- scene_aspectmode="data",
- scene_xaxis_showticklabels=session.show_ticks,
- scene_yaxis_showticklabels=session.show_ticks,
- scene_zaxis_showticklabels=session.show_ticks,
- scene_xaxis_visible=session.show_axis,
- scene_yaxis_visible=session.show_axis,
- scene_zaxis_visible=session.show_axis,
- hovermode=False,
- scene_camera_eye=dict(x=1.5, y=-1.5, z=1.2),
+ z_idx = int(session.zpos * session.vol_binary.shape[0])
+ fig = self.show_slice(
+ vol=session.vol_binary, z_idx=z_idx, cmap=session.cmap_originals
)
-
return fig
def compute_localthickness(self, session):
@@ -456,64 +333,12 @@ class Pipeline:
return session
- def prepare_output_for_display(self, session):
- # Display Local thickness
- session.vol_output_display = ndimage.zoom(
- input=session.vol_thickness,
- zoom=(session.display_size_output / session.max_size),
- prefilter=False,
- order=0,
- )
-
- output_display_shape = np.shape(session.vol_output_display)
- session.output_display_size_z = output_display_shape[0]
- session.output_display_size_y = output_display_shape[1]
- session.output_display_size_x = output_display_shape[2]
-
- session.Zgrid_output, session.Ygrid_output, session.Xgrid_output = np.mgrid[
- 0 : session.output_display_size_z,
- 0 : session.output_display_size_y,
- 0 : session.output_display_size_x,
- ]
-
- return session
-
def output_viz(self, session):
# Generate input visualization
- data = go.Volume(
- z=session.Zgrid_output.flatten(),
- y=session.Ygrid_output.flatten(),
- x=session.Xgrid_output.flatten(),
- value=session.vol_output_display.flatten(),
- opacity=0.3,
- isomin=0.05 * np.max(session.vol_output_display),
- isomax=1.0 * np.max(session.vol_output_display),
- cmin=np.min(session.vol_output_display),
- cmax=np.max(session.vol_output_display),
- opacityscale="uniform",
- surface_count=session.surface_count_input,
- caps=dict(
- x_show=session.show_caps,
- y_show=session.show_caps,
- z_show=session.show_caps,
- ),
- showscale=False,
- reversescale=session.reversescale,
+ z_idx = int(session.zpos * session.vol_thickness.shape[0])
+ fig = self.show_slice(
+ vol=session.vol_thickness, z_idx=z_idx, cmap=session.cmap_lt
)
-
- fig = go.Figure(data)
- fig.update_layout(
- scene_aspectmode="data",
- scene_xaxis_showticklabels=session.show_ticks,
- scene_yaxis_showticklabels=session.show_ticks,
- scene_zaxis_showticklabels=session.show_ticks,
- scene_xaxis_visible=session.show_axis,
- scene_yaxis_visible=session.show_axis,
- scene_zaxis_visible=session.show_axis,
- hovermode=False,
- scene_camera_eye=dict(x=1.5, y=-1.5, z=1.2),
- )
-
return fig
def thickness_histogram(self, session):
@@ -544,35 +369,3 @@ class Pipeline:
tifffile.imwrite(filename, session.vol_thickness)
return filename
-
-
-def gradio_fn(
- gradio_file,
- lt_scale,
- threshold,
- dark_objects,
- flip_z,
- nbins,
- display_size_input,
- surface_count_input,
- display_size_output,
- surface_count_output,
- reversescale,
- show_caps,
- show_ticks=False,
- show_axis=True,
-):
- # Some cleanup
- vol_input = None
- vol_input_display = None
- vol_output = None
- vol_output_display = None
- data = None
-
- return fig_input, fig_output, fig_binary, fig_hist, "localthickness.tif"
-
-
-if __name__ == "__main__":
- app = Interface()
- app.show_header = True
- app.launch(server_name="0.0.0.0", show_error=True)