+#!/usr/bin/env python
+# coding: utf-8
+
+# Copyright (c) Niivue.
+# Distributed under the terms of the Modified BSD License.
+
+# Much of the structure and many of the functions/classes in this file
+# are from https://github.com/martinRenou/ipycanvas. The Niivue class is based
+# off of Canvas class.
+
+# Standard library
+import json
+import math
+import pathlib
+import random
+import string
+import time
+import os
+from urllib.parse import urlparse
+from urllib.request import url2pathname
+
+# Third-party libraries
+from ipywidgets import DOMWidget
+from jupyter_ui_poll import ui_events
+from traitlets import (
+ Unicode,
+ CInt,
+ CFloat,
+ Dict,
+ List,
+ Bool,
+ UseEnum,
+ CaselessStrEnum,
+)
+
+# Local imports
+from .traits import (
+ DragModes,
+ SliceType,
+ keycodes,
+)
+from ._frontend import module_name, module_version
+from .nvimage import NVImage
+from .nvmesh import NVMesh
+
+class _CanvasBase(DOMWidget):
+ '''
+ Canvas
+
+ Parameters:
+ -----------
+ height: int
+ The height (in pixels) of the canvas
+ width: int
+ The width (in pixels) of the canvas
+ '''
+ _model_module = Unicode(module_name).tag(sync=True)
+ _model_module_version = Unicode(module_version).tag(sync=True)
+ _view_module = Unicode(module_name).tag(sync=True)
+ _view_module_version = Unicode(module_version).tag(sync=True)
+
+ height = CInt(480).tag(sync=True)
+ width = CInt(640).tag(sync=True)
+
+
+
+[docs]
+class Niivue(_CanvasBase):
+ '''
+ Niivue class.
+
+ Parameters:
+ -----------
+ text_height: float
+ the text height for orientation labels (0 to 1). Zero for no text
+ labels. Default is 0.06.
+ colorbar_height: float
+ size of colorbar. 0 for no colorbars, fraction of Nifti j dimension.
+ Default is 0.05.
+ colorbar_margin: float
+ padding around colorbar when displayed. Default is 0.05.
+ crosshair_width: float
+ crosshair size. Zero for no crosshair. Default is 1.
+ ruler_width: float
+ ruler size. 0 for no ruler. Default is 4.
+ back_color: list
+ the background color. RGBA values from 0 to 1. Default is
+ black ([0,0,0,1]).
+ crosshair_color: list
+ the crosshair color. RGBA values from 0 to 1. Default is
+ red ([1,0,0,1]).
+ selection_box_color: list
+ the selection box color when the intensty selection box is shown
+ (right click and drag). RGBA values from 0 to 1. Default is
+ transparent white ([1,1,1,0.5]).
+ clip_plane_color: list
+ the color of the visible clip plane. RGBA values from 0 to 1.
+ Default is white ([1,1,1,0.5]).
+ ruler_color: list
+ the color of the ruler. RGBA values from 0 to 1. Default is
+ translucent red ([1, 0, 0, 0.8]).
+ show_3D_crosshair: bool
+ True/False whether crosshairs are shown on 3D rendering.
+ Default is False.
+ trust_cal_min_max: bool
+ True/False whether to trust the nifti header values for
+ cal_min and cal_max. Trusting them results in faster loading
+ because we skip computing these values from the data.
+ Default is True.
+ clip_plane_hot_key: str
+ the keyboard key used to cycle through clip plane orientations.
+ Default is "KeyC".
+ view_mode_hot_key: str
+ the keyboard key used to cycle through view modes. Default is "KeyV".
+ key_debounce_time: float
+ the keyUp debounce time in milliseconds You must wait this long before
+ a new hot-key keystroke will be registered by the event listener.
+ The default is 50 ms.
+ double_touch_timeout: float
+ the maximum time in milliseconds for a double touch to be detected.
+ The default is 500 ms.
+ long_touch_timeout: float
+ the minimum time in milliseconds for a touch to count as long touch.
+ The default is 1000 ms.
+ is_radiological_convention: bool
+ whether or not to use radiological convention in the display.
+ Default is False.
+ loading_text: str
+ the loading text to display when there is a blank canvas and no images.
+ Default is "waiting on images...".
+ drag_and_drop_enabled: bool
+ whether or not to allow file and url drag and drop on the canvas.
+ Default is True.
+ is_nearest_interpolation: bool
+ whether nearest neighbor interpolation is used, else linear
+ interpolation. Default is False.
+ is_atlas_outline: bool
+ whether atlas maps are only visible at the boundary of regions.
+ Default is False.
+ is_ruler: bool
+ whether a 10cm ruler is displayed. Default is False.
+ is_colorbar: bool
+ whether colorbar(s) are shown illustrating values for color maps.
+ Default is False.
+ is_orient_cube: bool
+ whether orientation cube is shown for 3D renderings. Default is False.
+ multiplanar_pad_pixels: int
+ spacing between tiles of a multiplanar view. Default is 0.
+ mesh_thickness_on_2D: float
+ 2D slice views can show meshes within this range. Meshes only visible
+ in sliceMM (world space) mode. Default is Infinity.
+ drag_mode(str/int):
+ behavior for dragging. string ("none", "contrast",
+ "measurement", "pan", "slicer_3D") or integer (0, 1, 2, 3, 4).
+ Default is "contrast" or 1.
+ is_depth_pick_mesh: bool
+ when both voxel-based image and mesh is loaded, will depth picking be
+ able to detect mesh or only voxels. Default is False.
+ is_corner_orientation_text: bool
+ should slice text be shown in the upper right corner instead of the
+ center of left and top axes?. Default is False.
+ sagittal_nose_left: bool
+ should 2D sagittal slices show the anterior direction toward the
+ left?. Default is False.
+ is_slice_MM: bool
+ are images aligned to voxel space (False) or world space (True).
+ Default is False.
+ is_high_resolution_capable: bool
+ demand that high-dot-per-inch displays use native voxel size.
+ Default is True.
+ drawing_enabled: bool
+ allow user to create and edit voxel-based drawings.
+ Default is False.
+ pen_value: float
+ if drawing_enabled, color of drawing when user drags mouse.
+ Default is Infinity.
+ is_filled_pen: bool
+ if drawing_enabled, create filled drawings when user drags mouse.
+ Default is False.
+ max_draw_undo_bitmaps: int
+ if drawing_enabled, number of possible undo steps. Default is 8.
+ thumbnail: str
+ optional 2D png bitmap that can be rapidly loaded to defer slow
+ loading of 3D image. Default is "".
+ '''
+ _model_name = Unicode('NiivueModel').tag(sync=True)
+ _model_module = Unicode(module_name).tag(sync=True)
+ _model_module_version = Unicode(module_version).tag(sync=True)
+ _view_name = Unicode('NiivueView').tag(sync=True)
+ _view_module = Unicode(module_name).tag(sync=True)
+ _view_module_version = Unicode(module_version).tag(sync=True)
+
+ _custom_code_results = {}
+
+ # NiivueOptions
+ text_height = CFloat(default_value=0.06,
+ help="the text height for orientation labels (0 to 1)"
+ ". Zero for no text labels"
+ ).tag(sync=True)
+ colorbar_height = CFloat(default_value=0.05,
+ help="size of colorbar. 0 for no colorbars, "
+ "fraction of Nifti j dimension"
+ ).tag(sync=True)
+ colorbar_margin = CFloat(default_value=0.05,
+ help="padding around colorbar when displayed"
+ ).tag(sync=True)
+ crosshair_width = CFloat(default_value=1,
+ help="crosshair size. Zero for no crosshair"
+ ).tag(sync=True)
+ ruler_width = CFloat(default_value=4,
+ help="ruler size. 0 for no ruler"
+ ).tag(sync=True)
+ back_color = List(trait=CFloat(), default_value=(0, 0, 0, 1),
+ help="the background color. RGBA values from 0 to 1."
+ " Default is black"
+ ).tag(sync=True, min_len=4, max_len=4)
+ crosshair_color = List(trait=CFloat(), default_value=(1, 0, 0, 1),
+ help="the crosshair color. RGBA values from 0 to 1."
+ " Default is red"
+ ).tag(sync=True, min_len=4, max_len=4)
+ font_color = List(trait=CFloat(), default_value=(0.5, 0.5, 0.5, 1),
+ help="the font color. RGBA values from 0 to 1. Default "
+ "is gray"
+ ).tag(sync=True, min_len=4, max_len=4)
+ selection_box_color = List(trait=CFloat(), default_value=(1, 1, 1, 0.5),
+ help="the selection box color when the intensty"
+ " selection box is shown (right click and "
+ "drag). RGBA values from 0 to 1. Default "
+ "is transparent white"
+ ).tag(sync=True, min_len=4, max_len=4)
+ clip_plane_color = List(trait=CFloat(), default_value=(1, 1, 1, 0.5),
+ help="the color of the visible clip plane. RGBA "
+ "values from 0 to 1. Default is white"
+ ).tag(sync=True, min_len=4, max_len=4)
+ ruler_color = List(trait=CFloat(), default_value=(1, 0, 0, 0.8),
+ help="the color of the ruler. RGBA values from 0 to 1. "
+ "Default is translucent red"
+ ).tag(sync=True, min_len=4, max_len=4)
+ show_3D_crosshair = Bool(default_value=False,
+ help="True/False whether crosshairs are shown on "
+ "3D rendering"
+ ).tag(sync=True)
+ trust_cal_min_max = Bool(default_value=True,
+ help="True/False whether to trust the nifti "
+ "header values for cal_min and cal_max. "
+ "Trusting them results in faster loading "
+ "because we skip computing these values "
+ "from the data"
+ ).tag(sync=True)
+ clip_plane_hot_key = CaselessStrEnum(keycodes,
+ default_value="KeyC",
+ help="the keyboard key used to cycle"
+ " through clip plane "
+ "orientations"
+ ).tag(sync=True)
+ view_mode_hot_key = CaselessStrEnum(keycodes,
+ default_value="KeyV",
+ help="the keyboard key used to cycle "
+ "through view modes"
+ ).tag(sync=True)
+ key_debounce_time = CFloat(default_value=50,
+ help="the keyUp debounce time in milliseconds. "
+ "The default is 50 ms. You must wait this "
+ "long before a new hot-key keystroke will "
+ "be registered by the event listener"
+ ).tag(sync=True)
+ double_touch_timeout = CFloat(default_value=500,
+ help="the maximum time in milliseconds for a"
+ " double touch to be detected. The "
+ "default is 500 ms"
+ ).tag(sync=True)
+ long_touch_timeout = CFloat(default_value=1000,
+ help="the minimum time in milliseconds for a "
+ "touch to count as long touch. The "
+ "default is 1000 ms"
+ ).tag(sync=True)
+ is_radiological_convention = Bool(default_value=False,
+ help="whether or not to use radiological"
+ " convention in the display"
+ ).tag(sync=True)
+ loading_text = Unicode(default_value="waiting on images...",
+ help="the loading text to display when there is a "
+ "blank canvas and no images"
+ ).tag(sync=True)
+ drag_and_drop_enabled = Bool(default_value=True,
+ help="whether or not to allow file and url "
+ "drag and drop on the canvas"
+ ).tag(sync=True)
+ is_nearest_interpolation = Bool(default_value=False,
+ help="whether nearest neighbor "
+ "interpolation is used, else linear"
+ " interpolation"
+ ).tag(sync=True)
+ is_atlas_outline = Bool(default_value=False,
+ help="whether atlas maps are only visible at the"
+ " boundary of regions"
+ ).tag(sync=True)
+ is_ruler = Bool(default_value=False,
+ help="whether a 10cm ruler is displayed"
+ ).tag(sync=True)
+ is_colorbar = Bool(default_value=False,
+ help="whether colorbar(s) are shown illustrating values"
+ " for color maps"
+ ).tag(sync=True)
+ is_orient_cube = Bool(default_value=False,
+ help="whether orientation cube is shown for 3D "
+ "renderings"
+ ).tag(sync=True)
+ multiplanar_pad_pixels = CInt(default_value=0,
+ help="spacing between tiles of a multiplanar"
+ " view"
+ ).tag(sync=True)
+ multiplanar_force_render = Bool(default_value=False,
+ help="always show rendering in multiplanar"
+ " view"
+ ).tag(sync=True)
+ mesh_thickness_on_2D = CFloat(default_value=1.7976931348623157e+308,
+ help="2D slice views can show meshes within "
+ "this range. Meshes only visible in "
+ "slice_MM (world space) mode"
+ ).tag(sync=True)
+ drag_mode = UseEnum(DragModes, default_value=DragModes.contrast,
+ help='behavior for dragging ("none", "contrast", '
+ '"measurement", "pan", "slicer_3D")'
+ ).tag(sync=True)
+ is_depth_pick_mesh = Bool(default_value=False,
+ help="when both voxel-based image and mesh is "
+ "loaded, will depth picking be able to "
+ "detect mesh or only voxels"
+ ).tag(sync=True)
+ is_corner_orientation_text = Bool(default_value=False,
+ help="should slice text be shown in the"
+ " upper right corner instead of the"
+ " center of left and top axes?"
+ ).tag(sync=True)
+ sagittal_nose_left = Bool(default_value=False,
+ help="should 2D sagittal slices show the "
+ "anterior direction toward the left or"
+ " right?"
+ ).tag(sync=True)
+ is_slice_MM = Bool(default_value=False,
+ help="are images aligned to voxel space (False) or"
+ " world space (True)"
+ ).tag(sync=True)
+ is_high_resolution_capable = Bool(default_value=True,
+ help="demand that high-dot-per-inch "
+ "displays use native voxel size"
+ ).tag(sync=True)
+ drawing_enabled = Bool(default_value=False,
+ help="allow user to create and edit voxel-based"
+ " drawings"
+ ).tag(sync=True)
+ pen_value = CFloat(default_value=1.7976931348623157e+308,
+ help="color of drawing when user drags mouse "
+ "(if drawingEnabled)"
+ ).tag(sync=True)
+ is_filled_pen = Bool(default_value=False,
+ help="create filled drawings when user drags mouse "
+ "(if drawingEnabled)"
+ ).tag(sync=True)
+ max_draw_undo_bitmaps = CInt(default_value=8,
+ help="number of possible undo steps (if "
+ "drawingEnabled)"
+ ).tag(sync=True)
+ thumbnail = Unicode(default_value="",
+ help="optional 2D png bitmap that can be rapidly "
+ "loaded to defer slow loading of 3D image"
+ ).tag(sync=True)
+
+ slice_type = SliceType
+
+ def __init__(self, *args, **kwargs):
+ '''Create an Niivue widget.'''
+ super(Niivue, self).__init__(*args, **kwargs)
+ self.on_msg(self._handle_frontend_msg)
+ #todo: convert volumes and meshes into traitlets so that updates on the python side can be reflected on the ts side
+ self.volumes = []
+ self.meshes = []
+
+ def __str__(self):
+ return f'Niivue {self._model_id}'
+
+ def __repr__(self):
+ return f'ipyniivue.{super().__repr__()}'
+
+ def __dir__(self):
+ default = super().__dir__()
+ return [d for d in default if d not in dir(DOMWidget)]
+
+ def _handle_frontend_msg(self, _, content, buffers):
+ print('_handle_frontend_msg:', content, buffers)
+ event_data = content.get('event', [None])
+ if event_data[0] == 'customCodeResult':
+ code_id = event_data[1]
+ chunks_left = event_data[2]
+ if code_id not in self._custom_code_results:
+ self._custom_code_results[code_id] = {
+ 'chunks_left': -1, # placeholder. Correct value added
+ # after data processed.
+ 'result': b''
+ }
+
+ res = self._custom_code_results[code_id]
+ if len(buffers) > 0:
+ res['result'] += buffers[0].tobytes()
+
+ if chunks_left == 0:
+ if len(buffers) == 0 or res['result'] == b'undefined':
+ loaded = None
+ else:
+ loaded = json.loads(res['result'])
+ res['result'] = loaded
+
+ res['chunks_left'] = chunks_left
+ elif event_data[0] == 'updateVolumes':
+ partial_dict = json.loads(event_data[1])
+ volumes = [{**d, "dataBuffer": s.tobytes()} for d, s in zip(partial_dict, buffers)]
+ self.volumes = [NVImage(v) for v in volumes]
+ elif event_data[0] == 'updateMeshes':
+ self.meshes = [NVMesh(m) for m in json.loads(event_data[1])]
+
+ def _send_custom(self, command, buffers=[]):
+ self.send(command, buffers=buffers)
+
+
+[docs]
+ def save_scene(self, filename=''):
+ '''
+ Save the webgl2 canvas as png format bitmap.
+
+ Parameters:
+ -----------
+ filename: str
+ for screen capture.
+ '''
+ self._send_custom(['saveScene', [filename]])
+
+
+
+[docs]
+ def add_volume_from_url(self, url):
+ '''
+ Add an image from a url
+
+ Parameters:
+ -----------
+ url: str
+ The url link of the volume. Local paths and file urls are not
+ accepted.
+ '''
+ self._send_custom(['addVolumeFromUrl', [str(url)]])
+
+
+
+[docs]
+ def remove_volume_by_url(self, url):
+ '''
+ Remove volume by url. Local paths and file urls are not accepted.
+
+ Parameters:
+ -----------
+ url: str
+ Volume added by url to remove.
+ '''
+ self._send_custom(['removeVolumeByUrl', [str(url)]])
+
+
+
+[docs]
+ def set_text_orientation(self, is_at_corner):
+ '''
+ Set text appearance at corner (True) or sides of 2D slice (False).
+
+ Parameters:
+ -----------
+ is_at_corner: bool
+ does the text show at the corner (True) or sides of
+ 2D slice (False).
+ '''
+ self._send_custom(['setCornerOrientationText', [is_at_corner]])
+
+
+
+[docs]
+ def set_radiological_convention(self, is_radiological_convention):
+ '''
+ Control whether 2D slices use radiological or neurological convention.
+
+ Parameters:
+ -----------
+ is_radiological_convention: bool
+ use radiological convention.
+ '''
+ self._send_custom(['setRadiologicalConvention',
+ [is_radiological_convention]])
+
+
+
+[docs]
+ def set_mesh_thickness_on_2D(self, mesh_thickness_on_2D):
+ '''
+ Limit visibility of mesh in front of a 2D image.
+ Requires world-space mode.
+
+ Parameters:
+ -----------
+ mesh_thickness_on_2D: float
+ distance from voxels for clipping mesh. Use float('inf') to show
+ entire mesh or 0.0 to hide mesh.
+ '''
+ if math.isinf(mesh_thickness_on_2D):
+ mesh_thickness_on_2D = 1.7976931348623157e+308
+ self._send_custom(['setMeshThicknessOn2D', [mesh_thickness_on_2D]])
+
+
+
+[docs]
+ def set_slice_mosaic_string(self, description):
+ '''
+ Create a custom multi-slice mosaic (aka lightbox, montage) view.
+
+ Parameters:
+ -----------
+ description: str
+ description of mosaic. An example would be "A 0 20 C 30 S 42".
+ '''
+ self._send_custom(['setSliceMosaicString', [description]])
+
+
+
+[docs]
+ def set_slice_mm(self, is_slice_mm):
+ '''
+ determine view mode (world space or voxel space)
+
+ Parameters:
+ -----------
+ is_slice_mm: bool
+ Control whether 2D slices use world space (True) or voxel space
+ (False). Beware that voxel space mode limits properties like
+ panning, zooming and mesh visibility.
+ '''
+ self._send_custom(['setSliceMM', [is_slice_mm]])
+
+
+
+[docs]
+ def set_high_resolution_capable(self, is_high_resolution_capable):
+ '''
+ Force WebGL canvas to use high resolution display, regardless of
+ browser defaults.
+
+ Parameters:
+ -----------
+ is_high_resolution_capable: bool
+ allow high-DPI display
+ '''
+ self._send_custom(['setHighResolutionCapable',
+ [is_high_resolution_capable]])
+
+
+ """
+ def add_mesh(self, mesh):
+ '''
+ todo: Add a new mesh to the canvas.
+
+ Parameters:
+ -----------
+ mesh (todo)
+ '''
+ self._send_custom(['addMesh', [mesh]])
+ """
+
+
+[docs]
+ def undo_draw(self):
+ '''
+ Restore drawing to previous state
+ '''
+ self._send_custom(['drawUndo', []])
+
+
+
+[docs]
+ def load_drawing_from_url(self, url, is_binarize=False):
+ '''
+ Open drawing
+
+ Parameters:
+ -----------
+ url: str
+ the url
+ is_binarize: bool
+ binarize the drawing. Defaults to False.
+ '''
+ self._send_custom(['loadDrawingFromUrl', [str(url), is_binarize]])
+
+
+
+[docs]
+ def draw_otsu(self, levels):
+ '''
+ Remove dark voxels in air
+
+ Parameters:
+ -----------
+ levels: int
+ (2-4) segment brain into this many types
+ '''
+ self._send_custom(['drawOtsu', [levels]])
+
+
+
+[docs]
+ def remove_haze(self, level=5, vol_index=0):
+ '''
+ Remove dark voxels in air
+
+ Parameters:
+ -----------
+ level: int
+ (1-5) larger values for more preserved voxels
+ vol_index: int
+ volume to dehaze
+ '''
+ self._send_custom(['removeHaze', [level, vol_index]])
+
+
+
+[docs]
+ def save_image(self, filename, is_save_drawing=False):
+ '''
+ Save voxel-based image to disk
+
+ Parameters:
+ -----------
+ filename: str
+ filename of NIfTI image to create
+ is_save_drawing: bool
+ determines whether drawing or background image is saved
+ '''
+ self._send_custom(['saveImage', [filename, is_save_drawing]])
+
+
+
+[docs]
+ def set_mesh_property(self, mesh_id, key, value):
+ '''
+ Change property of mesh, tractogram or connectome
+
+ Parameters:
+ -----------
+ mesh_id: int
+ identity of mesh to change
+ key: str
+ attribute to change
+ value: float
+ for attribute
+ '''
+ self._send_custom(['setMeshProperty', [mesh_id, key, value]])
+
+
+
+[docs]
+ def reverse_faces(self, mesh_id):
+ '''
+ Reverse triangle winding of mesh (swap front and back faces)
+
+ Parameters:
+ -----------
+ mesh_id: int
+ identity of mesh to change
+ '''
+ self._send_custom(['reverseFaces', [mesh_id]])
+
+
+
+[docs]
+ def set_mesh_layer_property(self, mesh_id, layer, key, val):
+ '''
+ Reverse triangle winding of mesh (swap front and back faces)
+
+ Parameters:
+ -----------
+ mesh_id: int
+ identity of mesh to change
+ layer: int
+ selects the mesh overlay (e.g. GIfTI or STC file)
+ key: str
+ attribute to change
+ value: float
+ for attribute
+ '''
+ self._send_custom(['setMeshLayerProperty', [mesh_id, layer, key, val]])
+
+
+
+[docs]
+ def set_pan_2D_xyzmm(self, xyzmm_zoom):
+ '''
+ Adjust offset position and scale of 2D sliceScale
+
+ Parameters:
+ -----------
+ xyzmm_zoom: list
+ first three components are spatial, fourth is scaling
+ '''
+ self._send_custom(['setPan2Dxyzmm', [xyzmm_zoom]])
+
+
+
+[docs]
+ def set_render_azimuth_elevation(self, azimuth, elevation):
+ '''
+ Set rotation of 3D render view
+
+ Parameters:
+ -----------
+ azimuth: float
+ which direction/angle to face
+ elevation: float
+ how high up
+ '''
+ self._send_custom(['setRenderAzimuthElevation', [azimuth, elevation]])
+
+
+ """
+ #todo. Finish functions for adding volumes first. Model should also have
+ a volumes attribute.
+ def set_volume(self, volume, to_index = 0):
+ '''
+ todo: Set the index of a volume. This will change it's ordering and
+ appearance if there are multiple volumes loaded.
+
+ volume: todo
+ the volume to update
+ to_index: int
+ the index to move the volume to. The default is the background
+ (index 0)
+ '''
+ self._send_custom(['setVolume', [volume, to_index]])
+ """
+
+ """
+ #todo. Finish functions for adding volumes first. Model should also have
+ a volumes attribute.
+ def remove_volume(self, volume):
+ '''
+ todo: Remove a volume
+
+ Parameters:
+ -----------
+ volume: todo
+ volume to remove
+ '''
+ self._send_custom(['removeVolume', [volume]])
+ """
+
+
+[docs]
+ def remove_volume_by_index(self, index):
+ '''
+ Remove a volume by index
+
+ Parameters:
+ -----------
+ index: int
+ index of volume to remove
+ '''
+ self._send_custom(['removeVolumeByIndex', [index]])
+
+
+ """
+ #todo: Create a NVMesh class
+ def remove_mesh(self, mesh):
+ '''
+ todo: Remove a triangulated mesh, connectome or tractogram
+
+ Parameters:
+ -----------
+ mesh: todo
+ mesh to delete
+ '''
+ self._send_custom(['removeMesh', [mesh]])
+ """
+
+
+[docs]
+ def remove_mesh_by_url(self, url):
+ '''
+ Remove a triangulated mesh, connectome or tractogram
+
+ Parameters:
+ -----------
+ url: str
+ URL of mesh to delete
+ '''
+ self._send_custom(['removeMeshByUrl', [str(url)]])
+
+
+ """
+ #todo: create an NVImage class
+ def move_volume_to_bottom(self, volume):
+ '''
+ todo: Move a volume to the bottom of the stack of loaded volumes. The
+ volume will become the background
+
+ Parameters:
+ -----------
+ volume: todo
+ the volume to move
+ '''
+ self._send_custom(['moveVolumeToBottom', [volume]])
+
+ def move_volume_up(self, volume):
+ '''
+ todo: Move a volume up one index position in the stack of loaded
+ olumes. This moves it up one layer
+
+ Parameters:
+ -----------
+ volume: todo
+ the volume to move
+ '''
+ self._send_custom(['moveVolumeUp', [volume]])
+
+ def move_volume_down(self, volume):
+ '''
+ todo: Move a volume down one index position in the stack of loaded
+ volumes. This moves it down one layer
+
+ Parameters:
+ -----------
+ volume: todo
+ the volume to move
+ '''
+ self._send_custom(['moveVolumeDown', [volume]])
+
+ def move_volume_to_top(self, volume):
+ '''
+ todo: Move a volume to the top position in the stack of loaded
+ volumes. This will be the top layer
+
+ Parameters:
+ -----------
+ volume: todo
+
+ '''
+ self._send_custom(['moveVolumeToTop', [volume]])
+ """
+
+
+[docs]
+ def set_clip_plane(self, depth_azimuth_elevation):
+ '''
+ Update the clip plane orientation in 3D view mode
+
+ Parameters:
+ -----------
+ depth_azimuth_elevation: list
+ a two component vector: [azimuth, elevation]. azimuth: camera
+ position in degrees around object, typically 0..360
+ (or -180..+180). elevation: camera height in degrees, range -90..90
+ '''
+ self._send_custom(['setClipPlane', [depth_azimuth_elevation]])
+
+
+
+[docs]
+ def set_crosshair_color(self, color):
+ '''
+ Set the crosshair color
+
+ Parameters:
+ -----------
+ color: list
+ an RGBA array. Values range from 0 to 1
+ '''
+ self._send_custom(['setCrosshairColor', [color]])
+
+
+
+[docs]
+ def set_crosshair_width(self, crosshair_width):
+ '''
+ Set thickness of crosshair
+
+ Parameters:
+ -----------
+ crosshair_width: float
+ the crosshair width
+ '''
+ self._send_custom(['setCrosshairWidth', [crosshair_width]])
+
+
+
+[docs]
+ def set_drawing_enabled(self, drawing):
+ '''
+ Does dragging over a 2D slice create a drawing?
+
+ Parameters:
+ -----------
+ drawing: bool
+ enabled (True) or not (False)
+ '''
+ self._send_custom(['setDrawingEnabled', [drawing]])
+
+
+
+[docs]
+ def set_pen_value(self, pen_value, is_filled_pen=False):
+ '''
+ Determine color and style of drawing
+
+ Parameters:
+ -----------
+ pen_value: int
+ sets the color of the pen
+ is_filled_pen: bool
+ determines if dragging creates flood-filled shape
+ '''
+ self._send_custom(['setPenValue', [pen_value, is_filled_pen]])
+
+
+
+[docs]
+ def set_draw_opacity(self, opacity):
+ '''
+ Control whether drawing is transparent (0), opaque (1) or translucent
+ (between 0 and 1).
+
+ Parameters:
+ -----------
+ opacity: float
+ translucency of drawing. Transparent (0), opaque (1) or
+ translucent (between 0 and 1).
+ '''
+ self._send_custom(['setDrawOpacity', [opacity]])
+
+
+
+[docs]
+ def set_selection_box_color(self, color):
+ '''
+ Set the selection box color. A selection box is drawn when you right
+ click and drag to change image intensity
+
+ Parameters:
+ -----------
+ color: list
+ an RGBA array. Values range from 0 to 1.
+ '''
+ self._send_custom(['setSelectionBoxColor', [color]])
+
+
+
+[docs]
+ def set_slice_type(self, slice_type):
+ '''
+ Set the slice type. This changes the view mode
+
+ Parameters:
+ -----------
+ slice_type: int
+ the slice type. Valid values are nv.slice_type.axial,
+ nv.slice_type.coronal, nv.slice_type.sagittal,
+ nv.slice_type.multiplanar, and nv.slice_type.render
+ These are enumerated, so you can also input the values directly
+ (0-4), or you can input the strings ("axial", "coronal",
+ "sagittal", "multiplanar", "render").
+
+ '''
+ if isinstance(slice_type, str):
+ slice_type = slice_type.lower()
+ slice_type = getattr(self.slice_type, slice_type)
+ self._send_custom(['setSliceType', [slice_type]])
+
+
+
+[docs]
+ def set_opacity(self, vol_idx, new_opacity):
+ '''
+ Set the opacity of a volume given by volume index
+
+ Parameters:
+ -----------
+ vol_idx: int
+ the volume index of the volume to change
+ new_opacity: float
+ the opacity value. valid values range from 0 to 1. 0 will
+ effectively remove a volume from the scene
+ '''
+ self._send_custom(['setOpacity', [vol_idx, new_opacity]])
+
+
+
+[docs]
+ def set_scale(self, scale):
+ '''
+ Set the scale of the 3D rendering. Larger numbers effectively zoom.
+
+ Parameters:
+ -----------
+ scale: float
+ the new scale value
+ '''
+ self._send_custom(['setScale', [scale]])
+
+
+
+[docs]
+ def set_clip_plane_color(self, color):
+ '''
+ Set the color of the 3D clip plane
+
+ Parameters:
+ -----------
+ color: list
+ the new color. expects an array of RGBA values. values can range
+ from 0 to 1
+ '''
+ self._send_custom(['setClipPlaneColor', [color]])
+
+
+
+[docs]
+ def load_document_from_url(self, url):
+ '''
+ Load document from URL
+
+ Parameters:
+ -----------
+ url: str
+ URL of NVDocument
+ '''
+ self._send_custom(['loadDocumentFromUrl', [str(url)]])
+
+
+
+[docs]
+ def load_volumes(self, volume_list):
+ '''
+ load an array of volume objects
+
+ todo, allow for lists with mixed types (dictionaries and NVImage objects
+
+ Parameters:
+ -----------
+ volume_list: list
+ the array of objects to load
+ '''
+ if not isinstance(volume_list, list):
+ raise TypeError('volume_list must be a list')
+ if type(volume_list[0]) not in (dict, NVImage):
+ raise TypeError('volume_list must be a list of dictionaries or NVImage objects')
+
+ if len(volume_list) == 0:
+ return
+
+ if isinstance(volume_list[0], NVImage):
+ volume_list = [dict(v) for v in volume_list]
+ self._send_custom(['loadVolumes', [volume_list]])
+
+
+
+[docs]
+ def add_mesh_from_url(self, url):
+ '''
+ Add mesh from url
+
+ Parameters:
+ -----------
+ url: str
+ url of mesh
+ '''
+ self._send_custom(['addMeshFromUrl', [str(url)]])
+
+
+
+[docs]
+ def load_meshes(self, mesh_list):
+ '''
+ load an array of volume objects
+
+ todo, allow for lists with mixed types (dictionaries and NVImage objects
+
+ Parameters:
+ -----------
+ mesh_list: list
+ the array of objects to load
+ '''
+ if not isinstance(mesh_list, list):
+ raise TypeError('mesh_list must be a list')
+ if type(mesh_list[0]) not in (dict, NVMesh):
+ raise TypeError('mesh_list must be a list of dictionaries or NVMesh objects')
+
+ if len(mesh_list) == 0:
+ return
+
+ if isinstance(mesh_list[0], NVMesh):
+ mesh_list = [dict(v) for v in mesh_list]
+ self._send_custom(['loadMeshes', [mesh_list]])
+
+
+
+[docs]
+ def load_connectome(self, connectome):
+ '''
+ Load a connectome specified by dictionary/json
+
+ Parameters:
+ -----------
+ connectome: dict
+ connectome model
+ '''
+ self._send_custom(['loadConnectome', [connectome]])
+
+
+
+[docs]
+ def create_empty_drawing(self):
+ '''
+ Generate a blank canvas for the pen tool
+ '''
+ self._send_custom(['createEmptyDrawing', []])
+
+
+
+[docs]
+ def draw_grow_cut(self):
+ '''
+ Dilate drawing so all voxels are colored. works on drawing with
+ multiple colors
+ '''
+ self._send_custom(['drawGrowCut', []])
+
+
+
+[docs]
+ def set_mesh_shader(self, mesh_id, mesh_shader=2):
+ '''
+ Select new shader for triangulated meshes and connectomes
+
+ Parameters:
+ -----------
+ mesh_id: int
+ id of mesh to change
+ mesh_shader (str/int): identify shader for usage
+ '''
+ self._send_custom(['setMeshShader', [mesh_id, mesh_shader]])
+
+
+
+[docs]
+ def set_custom_mesh_shader(self, fragment_shader_text="", name="Custom"):
+ '''
+ Set custom shader for triangulated meshes and connectomes.
+
+ Parameters:
+ -----------
+ fragment_shader_text: str
+ custom fragment shader
+ name: str
+ title for new shader
+ '''
+ self._send_custom(['setCustomMeshShader',
+ [fragment_shader_text, name]])
+
+
+
+[docs]
+ def update_gl_volume(self):
+ '''
+ update the webGL 2.0 scene after making changes to the array of
+ volumes. Use if altering one or more volumes manually (outside of
+ Niivue setter methods).
+ '''
+ self._send_custom(['updateGLVolume', []])
+
+
+
+[docs]
+ def set_color_map(self, ID, color_map):
+ '''
+ Update the colormap of an image given its ID
+
+ Parameters:
+ -----------
+ ID: str
+ the ID of the image
+ color_map: str
+ the name of the color_map to use
+ '''
+ self._send_custom(['setColorMap', [ID, color_map]])
+
+
+
+[docs]
+ def set_color_map_negative(self, ID, color_map_negative):
+ '''
+ Use given color map for negative voxels in image
+
+ Parameters:
+ -----------
+ ID: str
+ the ID of the image
+ color_map_negative: str
+ the name of the color_map to use
+ '''
+ self._send_custom(['setColorMapNegative', [ID, color_map_negative]])
+
+
+
+[docs]
+ def set_modulation_image(self, id_target, id_modulation,
+ modulate_alpha=False):
+ '''
+ Modulate intensity of one image based on intensity of another
+
+ Parameters:
+ -----------
+ id_target: str
+ the ID of the image to be biased
+ id_modulation: str
+ the ID of the image that controls bias (None to disable modulation)
+ modulate_alpha: bool
+ the modulation influence alpha transparency (True) or RGB
+ color (False) components
+ '''
+ self._send_custom(['setModulationImage',
+ [id_target, id_modulation, modulate_alpha]])
+
+
+
+[docs]
+ def set_frame_4D(self, ID, frame_4D):
+ '''
+ Show desired 3D volume from 4D time series
+
+ Parameters:
+ -----------
+ ID: the ID of the 4D image
+ frame_4D: to display (indexed from zero)
+ '''
+ self._send_custom(['setFrame4D', [ID, frame_4D]])
+
+
+
+[docs]
+ def set_interpolation(self, is_nearest):
+ '''
+ Select between nearest and linear interpolation for voxel based images
+
+ Parameters:
+ -----------
+ is_nearest: bool
+ whether nearest neighbor interpolation is used, else linear
+ interpolation
+ '''
+ self._send_custom(['setInterpolation', [is_nearest]])
+
+
+
+[docs]
+ def move_crosshair_in_vox(self, x, y, z):
+ '''
+ Move crosshair a fixed number of voxels (instead of mm)
+
+ Parameters:
+ -----------
+ x: float
+ translate left (-) or right (+)
+ y: float
+ translate posterior (-) or +anterior (+)
+ z: float
+ translate inferior (-) or superior (+)
+ '''
+ self._send_custom(['moveCrosshairInVox', [x, y, z]])
+
+
+
+[docs]
+ def draw_mosaic(self, mosaic_str):
+ '''
+ Display a lightbox or montage view
+
+ Parameters:
+ -----------
+ mosaic_str: str
+ specifies orientation (A,C,S) and location of slices.
+ '''
+ self._send_custom(['drawMosaic', [mosaic_str]])
+
+
+
+[docs]
+ def add_volume(self, volume):
+ '''
+ Add a new volume to the canvas
+
+ Parameters:
+ -----------
+ volume: str or dict or NVImage
+ the path to the file (either url or local path)
+ '''
+ if isinstance(volume, str):
+ file = volume
+ if file.startswith('http://') or file.startswith('https://'):
+ self._send_custom(['addVolumeFromUrl', [{'url': str(file)}]])
+ else:
+ if file.startswith('file://'):
+ parsed = urlparse(file)
+ file = url2pathname(parsed.path)
+ p = pathlib.Path(file)
+ name = p.name
+ filedata = p.read_bytes()
+ self._send_custom(['addVolumeFromBase64', [name]], [filedata])
+ elif isinstance(volume, dict):
+ buffers = []
+ if 'dataBuffer' in volume:
+ buffers = [volume.pop('dataBuffer')]
+ self._send_custom(['addVolume', [volume]], buffers)
+ elif isinstance(volume, NVImage):
+ dict_volume = dict(volume)
+ buffers = []
+ if 'dataBuffer' in dict_volume:
+ buffers = [dict_volume.pop('dataBuffer')]
+ self._send_custom(['addVolume', [dict_volume]], buffers)
+
+
+
+[docs]
+ def add_object(self, img):
+ '''
+ Load a nibabel.nifti1.Nifti1Image object as a volume
+
+ Parameters:
+ -----------
+ img (nibabel.nifti1.Nifti1Image): Nifti1 image
+ '''
+ filename = (img.get_filename() or
+ ''.join(random.choice(string.ascii_uppercase +
+ string.digits)
+ for _ in range(20))
+ )
+ self._send_custom(['addVolumeFromBase64',
+ [os.path.basename(filename)]],
+ [img.to_bytes()])
+
+
+ # getter functions start here #
+
+[docs]
+ def run_custom_code(self, code, timeout=60, log=False):
+ '''
+ Run a custom JavaScript code snippet
+
+ Parameters:
+ -----------
+ code: str
+ the code to run
+ timeout: int
+ the maximum time to wait for the code to finish (in seconds)
+
+ Returns:
+ the result of the code
+ '''
+ code_id = ''.join(random.choice(string.ascii_uppercase +
+ string.digits)
+ for _ in range(20))
+ self._send_custom(['runCustomCode', [code_id]], [code.encode('utf-8')])
+
+ start = time.time()
+ i = 1
+ with ui_events() as poll:
+ while True:
+ poll(1)
+ # https://math.stackexchange.com/a/2678903
+ num = int(((i+2) % 3) + 1)
+ if log:
+ print(num * '.' + ' ', end='\r')
+ i += 0.25
+ time.sleep(0.1)
+ if time.time() - start > timeout or (
+ code_id in self._custom_code_results
+ and self._custom_code_results[code_id]["chunks_left"] == 0
+ ):
+ break
+ if log:
+ print("Done.")
+ result = self._custom_code_results.pop(code_id, {})
+ return result.get('result', None)
+
+
+
+[docs]
+ def get_descriptives(self, layer, masks):
+ '''
+ basic statistics for selected voxel-based image
+
+ Parameters:
+ -----------
+ layer: str
+ the ID of the image
+ masks: str
+ the ID of the mask
+
+ Returns:
+ --------
+ list
+ '''
+ code = f'this.nv.getDescriptives({layer}, {masks})'
+ return self.run_custom_code(code)
+
+
+
+[docs]
+ def get_frame_4D(self, ID):
+ '''
+ determine active 3D volume from 4D time series
+
+ Parameters:
+ -----------
+ ID: str
+ the ID of the 4D image
+
+ Returns:
+ --------
+ int
+ '''
+ return self.run_custom_code(f'this.nv.getFrame4D({ID})')
+
+
+
+[docs]
+ def get_media_by_url(self, url):
+ '''
+ Find media by url
+
+ Parameters:
+ -----------
+ url: str
+
+ Returns:
+ --------
+ NVImage or NVMesh
+ '''
+ return self.run_custom_code(f'this.nv.getMediaByUrl({url})')
+
+
+
+[docs]
+ def get_overlay_index_by_ID(self, ID):
+ '''
+ get the index of an overlay by its unique id. unique ids are assigned
+ to the NVImage.id property when a new NVImage is created.
+
+ Parameters:
+ -----------
+ ID: str
+ the ID of the overlay
+
+ Returns:
+ --------
+ int
+ '''
+ return self.run_custom_code(f'this.nv.getOverlayIndexByID({ID})')
+
+
+
+[docs]
+ def get_radiological_convention(self):
+ '''
+ Detect if display is using radiological or neurological convention.
+
+ Returns:
+ --------
+ bool
+ '''
+ return self.run_custom_code('this.nv.getRadiologicalConvention()')
+
+
+
+[docs]
+ def get_volume_index_by_ID(self, ID):
+ '''
+ get the index of a volume by its unique id. unique ids are assigned to
+ the NVImage.id property when a new NVImage is created.
+
+ Parameters:
+ -----------
+ ID: str
+ the ID of the volume
+
+ Returns:
+ --------
+ int
+ '''
+ return self.run_custom_code(f'this.nv.getVolumeIndexByID({ID})')
+
+
+
+[docs]
+ def is_mesh_ext(self, url):
+ '''
+ Returns boolean: true if filename ends with mesh
+ extension (TRK, pial, etc.)
+
+ Parameters:
+ -----------
+ url: str
+ the url or filepath of the mesh
+
+ Returns:
+ --------
+ bool
+ '''
+ return self.run_custom_code(f'this.nv.isMeshExt({url})')
+
+
+Niivue class.
+the text height for orientation labels (0 to 1). Zero for no text +labels. Default is 0.06.
+size of colorbar. 0 for no colorbars, fraction of Nifti j dimension. +Default is 0.05.
+padding around colorbar when displayed. Default is 0.05.
+crosshair size. Zero for no crosshair. Default is 1.
+ruler size. 0 for no ruler. Default is 4.
+the background color. RGBA values from 0 to 1. Default is +black ([0,0,0,1]).
+the crosshair color. RGBA values from 0 to 1. Default is +red ([1,0,0,1]).
+the selection box color when the intensty selection box is shown +(right click and drag). RGBA values from 0 to 1. Default is +transparent white ([1,1,1,0.5]).
+the color of the visible clip plane. RGBA values from 0 to 1. +Default is white ([1,1,1,0.5]).
+the color of the ruler. RGBA values from 0 to 1. Default is +translucent red ([1, 0, 0, 0.8]).
+True/False whether crosshairs are shown on 3D rendering. +Default is False.
+True/False whether to trust the nifti header values for +cal_min and cal_max. Trusting them results in faster loading +because we skip computing these values from the data. +Default is True.
+the keyboard key used to cycle through clip plane orientations. +Default is “KeyC”.
+the keyboard key used to cycle through view modes. Default is “KeyV”.
+the keyUp debounce time in milliseconds You must wait this long before +a new hot-key keystroke will be registered by the event listener. +The default is 50 ms.
+the maximum time in milliseconds for a double touch to be detected. +The default is 500 ms.
+the minimum time in milliseconds for a touch to count as long touch. +The default is 1000 ms.
+whether or not to use radiological convention in the display. +Default is False.
+the loading text to display when there is a blank canvas and no images. +Default is “waiting on images…”.
+whether or not to allow file and url drag and drop on the canvas. +Default is True.
+whether nearest neighbor interpolation is used, else linear +interpolation. Default is False.
+whether atlas maps are only visible at the boundary of regions. +Default is False.
+whether a 10cm ruler is displayed. Default is False.
+whether colorbar(s) are shown illustrating values for color maps. +Default is False.
+whether orientation cube is shown for 3D renderings. Default is False.
+spacing between tiles of a multiplanar view. Default is 0.
+2D slice views can show meshes within this range. Meshes only visible +in sliceMM (world space) mode. Default is Infinity.
+behavior for dragging. string (“none”, “contrast”, +“measurement”, “pan”, “slicer_3D”) or integer (0, 1, 2, 3, 4). +Default is “contrast” or 1.
+when both voxel-based image and mesh is loaded, will depth picking be +able to detect mesh or only voxels. Default is False.
+should slice text be shown in the upper right corner instead of the +center of left and top axes?. Default is False.
+should 2D sagittal slices show the anterior direction toward the +left?. Default is False.
+are images aligned to voxel space (False) or world space (True). +Default is False.
+demand that high-dot-per-inch displays use native voxel size. +Default is True.
+allow user to create and edit voxel-based drawings. +Default is False.
+if drawing_enabled, color of drawing when user drags mouse. +Default is Infinity.
+if drawing_enabled, create filled drawings when user drags mouse. +Default is False.
+if drawing_enabled, number of possible undo steps. Default is 8.
+optional 2D png bitmap that can be rapidly loaded to defer slow +loading of 3D image. Default is “”.
+Add mesh from url
+url of mesh
+Load a nibabel.nifti1.Nifti1Image object as a volume
+img (nibabel.nifti1.Nifti1Image): Nifti1 image
+Add a new volume to the canvas
+the path to the file (either url or local path)
+Add an image from a url
+The url link of the volume. Local paths and file urls are not +accepted.
+the background color. RGBA values from 0 to 1. Default is black
+the color of the visible clip plane. RGBA values from 0 to 1. Default is white
+the keyboard key used to cycle through clip plane orientations
+size of colorbar. 0 for no colorbars, fraction of Nifti j dimension
+padding around colorbar when displayed
+the crosshair color. RGBA values from 0 to 1. Default is red
+crosshair size. Zero for no crosshair
+the maximum time in milliseconds for a double touch to be detected. The default is 500 ms
+whether or not to allow file and url drag and drop on the canvas
+behavior for dragging (“none”, “contrast”, “measurement”, “pan”, “slicer_3D”)
+Dilate drawing so all voxels are colored. works on drawing with +multiple colors
+Display a lightbox or montage view
+specifies orientation (A,C,S) and location of slices.
+Remove dark voxels in air
+(2-4) segment brain into this many types
+allow user to create and edit voxel-based drawings
+the font color. RGBA values from 0 to 1. Default is gray
+basic statistics for selected voxel-based image
+the ID of the image
+the ID of the mask
+list
+determine active 3D volume from 4D time series
+the ID of the 4D image
+int
+Find media by url
+url: str
+NVImage or NVMesh
+get the index of an overlay by its unique id. unique ids are assigned +to the NVImage.id property when a new NVImage is created.
+the ID of the overlay
+int
+Detect if display is using radiological or neurological convention.
+bool
+get the index of a volume by its unique id. unique ids are assigned to +the NVImage.id property when a new NVImage is created.
+the ID of the volume
+int
+whether atlas maps are only visible at the boundary of regions
+whether colorbar(s) are shown illustrating values for color maps
+should slice text be shown in the upper right corner instead of the center of left and top axes?
+when both voxel-based image and mesh is loaded, will depth picking be able to detect mesh or only voxels
+create filled drawings when user drags mouse (if drawingEnabled)
+demand that high-dot-per-inch displays use native voxel size
+extension (TRK, pial, etc.)
+the url or filepath of the mesh
+bool
+whether nearest neighbor interpolation is used, else linear interpolation
+whether orientation cube is shown for 3D renderings
+whether or not to use radiological convention in the display
+whether a 10cm ruler is displayed
+are images aligned to voxel space (False) or world space (True)
+the keyUp debounce time in milliseconds. The default is 50 ms. You must wait this long before a new hot-key keystroke will be registered by the event listener
+Load a connectome specified by dictionary/json
+connectome model
+Load document from URL
+URL of NVDocument
+Open drawing
+the url
+binarize the drawing. Defaults to False.
+load an array of volume objects
+todo, allow for lists with mixed types (dictionaries and NVImage objects
+the array of objects to load
+load an array of volume objects
+todo, allow for lists with mixed types (dictionaries and NVImage objects
+the array of objects to load
+the loading text to display when there is a blank canvas and no images
+the minimum time in milliseconds for a touch to count as long touch. The default is 1000 ms
+number of possible undo steps (if drawingEnabled)
+2D slice views can show meshes within this range. Meshes only visible in slice_MM (world space) mode
+Move crosshair a fixed number of voxels (instead of mm)
+translate left (-) or right (+)
+translate posterior (-) or +anterior (+)
+translate inferior (-) or superior (+)
+always show rendering in multiplanar view
+spacing between tiles of a multiplanar view
+color of drawing when user drags mouse (if drawingEnabled)
+Remove dark voxels in air
+(1-5) larger values for more preserved voxels
+volume to dehaze
+Remove a triangulated mesh, connectome or tractogram
+URL of mesh to delete
+Remove a volume by index
+index of volume to remove
+Remove volume by url. Local paths and file urls are not accepted.
+Volume added by url to remove.
+Reverse triangle winding of mesh (swap front and back faces)
+identity of mesh to change
+the color of the ruler. RGBA values from 0 to 1. Default is translucent red
+ruler size. 0 for no ruler
+Run a custom JavaScript code snippet
+the code to run
+the maximum time to wait for the code to finish (in seconds)
+the result of the code
+should 2D sagittal slices show the anterior direction toward the left or right?
+Save voxel-based image to disk
+filename of NIfTI image to create
+determines whether drawing or background image is saved
+Save the webgl2 canvas as png format bitmap.
+for screen capture.
+the selection box color when the intensty selection box is shown (right click and drag). RGBA values from 0 to 1. Default is transparent white
+Update the clip plane orientation in 3D view mode
+a two component vector: [azimuth, elevation]. azimuth: camera +position in degrees around object, typically 0..360 +(or -180..+180). elevation: camera height in degrees, range -90..90
+Set the color of the 3D clip plane
+the new color. expects an array of RGBA values. values can range +from 0 to 1
+Update the colormap of an image given its ID
+the ID of the image
+the name of the color_map to use
+Use given color map for negative voxels in image
+the ID of the image
+the name of the color_map to use
+Set the crosshair color
+an RGBA array. Values range from 0 to 1
+Set thickness of crosshair
+the crosshair width
+Set custom shader for triangulated meshes and connectomes.
+custom fragment shader
+title for new shader
+Control whether drawing is transparent (0), opaque (1) or translucent +(between 0 and 1).
+translucency of drawing. Transparent (0), opaque (1) or +translucent (between 0 and 1).
+Does dragging over a 2D slice create a drawing?
+enabled (True) or not (False)
+Show desired 3D volume from 4D time series
+frame_4D: to display (indexed from zero)
+Force WebGL canvas to use high resolution display, regardless of +browser defaults.
+allow high-DPI display
+Select between nearest and linear interpolation for voxel based images
+whether nearest neighbor interpolation is used, else linear +interpolation
+Reverse triangle winding of mesh (swap front and back faces)
+identity of mesh to change
+selects the mesh overlay (e.g. GIfTI or STC file)
+attribute to change
+for attribute
+Change property of mesh, tractogram or connectome
+identity of mesh to change
+attribute to change
+for attribute
+Select new shader for triangulated meshes and connectomes
+id of mesh to change +mesh_shader (str/int): identify shader for usage
+Limit visibility of mesh in front of a 2D image. +Requires world-space mode.
+distance from voxels for clipping mesh. Use float(‘inf’) to show +entire mesh or 0.0 to hide mesh.
+Modulate intensity of one image based on intensity of another
+the ID of the image to be biased
+the ID of the image that controls bias (None to disable modulation)
+the modulation influence alpha transparency (True) or RGB +color (False) components
+Set the opacity of a volume given by volume index
+the volume index of the volume to change
+the opacity value. valid values range from 0 to 1. 0 will +effectively remove a volume from the scene
+Adjust offset position and scale of 2D sliceScale
+first three components are spatial, fourth is scaling
+Determine color and style of drawing
+sets the color of the pen
+determines if dragging creates flood-filled shape
+Control whether 2D slices use radiological or neurological convention.
+use radiological convention.
+Set rotation of 3D render view
+which direction/angle to face
+how high up
+Set the scale of the 3D rendering. Larger numbers effectively zoom.
+the new scale value
+Set the selection box color. A selection box is drawn when you right +click and drag to change image intensity
+an RGBA array. Values range from 0 to 1.
+determine view mode (world space or voxel space)
+Control whether 2D slices use world space (True) or voxel space +(False). Beware that voxel space mode limits properties like +panning, zooming and mesh visibility.
+Create a custom multi-slice mosaic (aka lightbox, montage) view.
+description of mosaic. An example would be “A 0 20 C 30 S 42”.
+Set the slice type. This changes the view mode
+the slice type. Valid values are nv.slice_type.axial, +nv.slice_type.coronal, nv.slice_type.sagittal, +nv.slice_type.multiplanar, and nv.slice_type.render +These are enumerated, so you can also input the values directly +(0-4), or you can input the strings (“axial”, “coronal”, +“sagittal”, “multiplanar”, “render”).
+Set text appearance at corner (True) or sides of 2D slice (False).
+does the text show at the corner (True) or sides of +2D slice (False).
+True/False whether crosshairs are shown on 3D rendering
+alias of SliceType
the text height for orientation labels (0 to 1). Zero for no text labels
+optional 2D png bitmap that can be rapidly loaded to defer slow loading of 3D image
+True/False whether to trust the nifti header values for cal_min and cal_max. Trusting them results in faster loading because we skip computing these values from the data
+update the webGL 2.0 scene after making changes to the array of +volumes. Use if altering one or more volumes manually (outside of +Niivue setter methods).
+the keyboard key used to cycle through view modes
+