The modeless dialog held a raw Node pointer, so deleting the node
while the dialog was open left OK/Apply dereferencing freed memory
and crashing in markStale(). Close the dialog on nodeRemoved and
hold the node in a QPointer so the pointer can never dangle.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

RescaleTransferFunction operates on the proxy property, which still
contained the placeholder nodes spanning the full data range, making
Reset a no-op and Auto compress the window. Sync the stripped client
state first, and match ImageJ's auto-threshold progression.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

better link selection and other quality of life improvements

Target the scroll area and container by name so the strip's context
menus keep native rendering, and use stable_sort so keyboard
navigation order is deterministic on ties.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

This is important to fix an issue where a different version of h5py was
being imported from the user site-packages directory, which was causing
tomviz to crash.

Also delay trying to import ptycho and pyxrf until the user triggers the
action.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

This explains how to maintain pyxrf-utils

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Operators whose dependencies (e.g. PyTorch) can never be imported in
the application environment can declare "externalOnly": true in their
JSON description. Fresh nodes then default to the External executor,
the editor disables the Internal choice, and a missing environment is
reported with an actionable message instead of a console warning.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Add a built-in, external-only operator that segments a 3D volume with
Meta's SAM 2 by propagating a seed-slice prompt along the Z axis. The
conda environment files it needs ship under share/tomviz/environments,
and a guarded import reports full setup instructions when sam2 is
missing. Model checkpoints are user-downloaded, not bundled.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

This allows help buttons to be displayed that explain the operator.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Otherwise, it produces empty output with the example data

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

On an IC ptychography tomogram, features are only recognized as
"bright lines" from side views, so a 2-of-3 vote discarded nearly half
of the real detections. Default to a vote threshold of 1 and offset
the looser voting with a larger minimum component size. The default
prompt is dataset-dependent either way and usually needs a quick
per-dataset experiment; the docs now say so.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Both operators produce categorical label maps, so declare the output
port type accordingly: downstream nodes see a LabelMap port and the
volume sink applies its label-map rendering defaults.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Typing voxel indices was a poor proxy for SAM's click-first prompting,
and the quality of the seed is the main determinant of the result.
SAM2SeedWidget shows a slice of the input volume in the operator
dialog: left-click sets Seed X/Y, a slider drives Seed Z, the Z Axis
choice controls the slicing direction, the wheel zooms about the
cursor, and a right-drag pans. The widget embeds the standard
JSON-driven form rather than duplicating it, and the seed round-trips
through the existing seed_x/y/z parameters, so serialization and
external execution are unchanged. Point mode becomes the default
prompt mode, matching the new interaction (and the Python default).

Offscreen gtests cover the form embedding, click-to-voxel mapping,
slider/seed sync, axis switching, value restore, and zoom anchoring.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Applying an external executor now stores its environment path in
QSettings keyed by the operator's JSON name, and a node with no
configured executor starts with the remembered path prefilled. The
SAM 2 / SAM 3 conda environments (and any other external operator's)
only need to be picked once; a node's own configured path always wins
over the remembered one.

Also derive the env-path row's initial enabled state from the executor
combo rather than the node's executor type: a fresh externalOnly node
shows External selected but previously left the path row disabled.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Avoid a shared QApplication helper /proc/self/exe, which only works
on Linux.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

After the seeded object ends, the video tracker can reattach to other
bright objects, leaving phantom regions. Trim the mask below an
intensity floor and keep only the seed-connected component, both on by
default.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Render the seed slice through the volume's color transfer function and
observe its ModifiedEvent, so the dialog matches the main window's
colormap and follows edits live. Falls back to a grayscale stretch when
no ParaView session exists.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Replace seed_x/y/z with a single vector seed parameter so the three
spinboxes share one row, like Shift3D. Values saved under the old
parameter names fall back to the default seed.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

vtkVolume::RenderVolumetricGeometry() updates the mapper before its own
no-input check, so a visible but empty volume logs a spurious pipeline
error on every render. State load restored visibility ahead of the
threaded pipeline execution, which is where it showed up.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

The buttons only refreshed on view changes, and port selection nulls
the active node, so they could latch disabled with no way back. Enable
them whenever a valid LUT is present, refresh on every setLUTProxy
call, and clear the proxy when the selection has no colormap.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

This allows components which have a very thin connection to be
labeled separately. It's an optional parameter.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

They were not being added or applied correctly, and label maps were
not resetting the range.

This should all work fine now.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Matching the main window's colormap called colorMap(), which creates one
when absent, leaving the input volume with an unrescaled default it never
had. Use it only if it already exists; otherwise fall back to grayscale.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Setting port data drives the sinks, so an externally-executed label map
was rendered through the upstream volume's colormap before its own
segmentation colormap existed: miscolored, with a GPU lookup table VTK
had to clamp. TransformNode::execute already does this for internal nodes.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>