pyproject.toml

[build-system]
requires = ["setuptools", "ChimeraX-BundleBuilder"]
build-backend = "chimerax.bundle_builder.cx_pep517"

[project]
name = "ChimeraX-MedicalImaging"
license = { text = "Free for non-commercial use" }
authors = [{ name = "UCSF RBVI", email = "chimerax@cgl.ucsf.edu" }]
description = "Medical imaging support including DICOM format"
dependencies = [
  "ChimeraX-Core ~=1.0",
  "ChimeraX-DataFormats ~=1.0",
  "ChimeraX-Geometry ~= 1.0",
  "ChimeraX-MapData ~= 2.0",
  "ChimeraX-OpenCommand ~= 1.0",
  "ChimeraX-UI >= 1.33",
]
dynamic = ["classifiers", "requires-python", "version"]

[project.optional-dependencies]
losslessjpeg = ["python-gdcm"]

[project.readme]
content-type = "text"
text = "Medical imaging support for ChimeraX, including DICOM format reading/writing and medical image visualization tools."

[project.urls]
Home = "https://www.rbvi.ucsf.edu/chimerax/"

[tool.setuptools.dynamic]
version = { attr = "src.__version__" }

[tool.chimerax]
custom-init = true
min-session-version = 1
max-session-version = 1
categories = ["Medical Imaging"]
classifiers = ["Development Status :: 2 - Pre-Alpha"]
supersedes = ["ChimeraX-Dicom", "ChimeraX-MedicalToolbar"]

[tool.chimerax.package-data]
"src/icons" = ["*.png"]

# ----------------- Data Formats -----------------
[tool.chimerax.data-format."DICOM medical imaging"]
category = "Medical Imaging"
nicknames = ["dicom"]
suffixes = [".dcm"]
allow-directory = true
synopsis = "DICOM"

[[tool.chimerax.data-format."DICOM medical imaging".open]]
batch = true

[[tool.chimerax.data-format."DICOM medical imaging".open]]
type = "fetch"
name = "tcia"
format-name = "dicom"
is-default = false

[[tool.chimerax.data-format."DICOM medical imaging".save]]
compression-okay = false
is-default = true

# ----------------- Tools -----------------
[tool.chimerax.tool."DICOM Browser"]
category = "Medical Imaging"
description = "View the metadata of a patient's DICOM files"

[tool.chimerax.tool."Download DICOM"]
category = "Medical Imaging"
description = "View the contents of public DICOM datasets from within ChimeraX"

# ----------------- Toolbars -----------------
[tool.chimerax.toolbar."Medical Image"]
after = "Map"
before = "Markers:Right Mouse"

[tool.chimerax.toolbar."Medical Image".sections."File"]

[[tool.chimerax.toolbar."Medical Image".sections."File".button]]
name = "open dicom"
display-name = "Open DICOM"
icon = "opendicom.png"
description = "Open DICOM directories"

[[tool.chimerax.toolbar."Medical Image".sections."File".button]]
name = "recent"
link = "ChimeraX-Toolbar:Recent"

[[tool.chimerax.toolbar."Medical Image".sections."File".button]]
name = "snapshot"
link = "ChimeraX-Shortcuts:sx"

[tool.chimerax.toolbar."Medical Image".sections."Style"]
after = "File"

[[tool.chimerax.toolbar."Medical Image".sections."Style".button]]
name = "plane style"
link = "ChimeraX-Shortcuts:pl"

[[tool.chimerax.toolbar."Medical Image".sections."Style".button]]
name = "slab style"
link = "ChimeraX-Shortcuts:is"

[[tool.chimerax.toolbar."Medical Image".sections."Style".button]]
name = "orthoplanes style"
link = "ChimeraX-Shortcuts:o3"

[[tool.chimerax.toolbar."Medical Image".sections."Style".button]]
name = "full style"
link = "ChimeraX-Shortcuts:pa"

[[tool.chimerax.toolbar."Medical Image".sections."Style".button]]
name = "outline box"
link = "ChimeraX-Shortcuts:ob"

[tool.chimerax.toolbar."Medical Image".sections."Color"]
after = "Style"

[[tool.chimerax.toolbar."Medical Image".sections."Color".button]]
name = "airways"
link = "ChimeraX-Shortcuts:aw"

[[tool.chimerax.toolbar."Medical Image".sections."Color".button]]
name = "chest"
link = "ChimeraX-Shortcuts:ch"

[[tool.chimerax.toolbar."Medical Image".sections."Color".button]]
name = "brain"
link = "ChimeraX-Shortcuts:bc"

[[tool.chimerax.toolbar."Medical Image".sections."Color".button]]
name = "default thresholds"
link = "ChimeraX-Shortcuts:dc"

[tool.chimerax.toolbar."Medical Image".sections."Graphics"]
after = "Color"

[[tool.chimerax.toolbar."Medical Image".sections."Graphics".button]]
name = "orient"
link = "ChimeraX-Shortcuts:dv"

[[tool.chimerax.toolbar."Medical Image".sections."Graphics".button]]
name = "step 1"
link = "ChimeraX-Shortcuts:s1"

[[tool.chimerax.toolbar."Medical Image".sections."Graphics".button]]
name = "step 2"
link = "ChimeraX-Shortcuts:s2"

[tool.chimerax.toolbar."Medical Image".sections."Rendering Modes"]
after = "Graphics"

[[tool.chimerax.toolbar."Medical Image".sections."Rendering Modes".button]]
name = "xyz slices"
link = "ChimeraX-Shortcuts:zs"

[[tool.chimerax.toolbar."Medical Image".sections."Rendering Modes".button]]
name = "perpendicular slices"
link = "ChimeraX-Shortcuts:ps"

[[tool.chimerax.toolbar."Medical Image".sections."Rendering Modes".button]]
name = "raycasting"
link = "ChimeraX-Shortcuts:rs"

[tool.chimerax.toolbar."Medical Image".sections."Mouse Mode"]
after = "Rendering Modes"

[[tool.chimerax.toolbar."Medical Image".sections."Mouse Mode".button]]
name = "mm1"
mouse-mode = "crop volume"
display-name = "Crop"
description = "Crop volume data dragging any face of box outline"

[[tool.chimerax.toolbar."Medical Image".sections."Mouse Mode".button]]
name = "mm2"
mouse-mode = "move planes"
display-name = "Move planes"
description = "Move plane or slab along its axis to show a different section"

[[tool.chimerax.toolbar."Medical Image".sections."Mouse Mode".button]]
name = "mm3"
mouse-mode = "rotate slab"
display-name = "Tilt slab"
description = "Tilt image planes, hold shift key to translate"

[[tool.chimerax.toolbar."Medical Image".sections."Mouse Mode".button]]
name = "mm4"
mouse-mode = "tape measure"
display-name = "Tape"
description = "Measure distance between two points"

[[tool.chimerax.toolbar."Medical Image".sections."Mouse Mode".button]]
name = "mm5"
mouse-mode = "windowing"
display-name = "Windowing"
description = "Adjust volume data thresholds collectively"