370 lines (300 with data), 14.2 kB
#!/usr/bin/env python
import pkgutil
import threading
import click
import numpy as np
import glfw
import OpenGL.GL as gl
import OpenGL.GL.ARB.texture_float
from os.path import dirname, realpath, join
from PIL import Image, ImageFont
from contextlib import contextmanager
from functools import lru_cache
from os.path import join, dirname
__version__ = "3.0.2"
# -----------------------------------------------------------------------------
@click.command()
@click.argument('slide', metavar='PATH', required=False)
@click.option('--model', '-m', help='Classifier network for categorical predictions.', metavar='PATH')
@click.option('--project', '-p', help='Slideflow project.', metavar='PATH')
@click.option('--low_memory', '-l', is_flag=True, help='Low memory mode.', metavar=bool)
@click.option('--stylegan', '-g', is_flag=True, help='Enable StyleGAN support (requires PyTorch).', metavar=bool)
@click.option('--picam', '-pc', is_flag=True, help='Enable Picamera2 view (experimental).', metavar=bool)
@click.option('--camera', '-c', is_flag=True, help='Enable Camera (OpenCV) view (experimental).', metavar=bool)
@click.option('--cellpose', is_flag=True, help='Enable Cellpose segmentation (experimental).', metavar=bool)
def main(
slide,
model,
project,
low_memory,
stylegan,
picam,
camera,
cellpose
):
"""
Whole-slide image viewer with deep learning model visualization tools.
Optional PATH argument can be used specify which slide to initially load.
"""
# Start the splash screen
import_with_splash()
from slideflow.studio import Studio
if low_memory is None:
low_memory = False
# Load widgets
widgets = Studio.get_default_widgets()
if stylegan:
from slideflow.studio.widgets.stylegan import StyleGANWidget
widgets += [StyleGANWidget]
if picam:
from slideflow.studio.widgets.picam import PicamWidget
widgets += [PicamWidget]
if camera:
from slideflow.studio.widgets.cvcam import CameraWidget
widgets += [CameraWidget]
if cellpose:
from slideflow.studio.widgets.cellseg import CellSegWidget
widgets += [CellSegWidget]
viz = Studio(low_memory=low_memory, widgets=widgets)
viz.project_widget.search_dirs += [dirname(realpath(__file__))]
# Load model.
if model is not None:
viz.load_model(model)
if project is not None:
viz.load_project(project)
# Load slide(s).
if slide:
viz.load_slide(slide)
# Run.
viz.run()
#----------------------------------------------------------------------------
def import_with_splash():
_imported = False
def _import_sildeflow():
nonlocal _imported
import slideflow.studio
_imported = True
# Start the import thread
_thread = threading.Thread(target=_import_sildeflow)
_thread.start()
# Send Tk to the background (used for future file dialogs)
from tkinter import Tk
Tk().withdraw()
# Load image
sf_root = pkgutil.get_loader('slideflow').get_filename()
splash_path = join(dirname(sf_root), 'studio', 'gui', 'splash.png')
icon_path = join(dirname(sf_root), 'studio', 'gui', 'icons', 'logo.png')
img = np.array(Image.open(splash_path))
icon = np.array(Image.open(icon_path))
# Start GLFW window
if not glfw.init():
return
glfw.window_hint(glfw.DECORATED, False)
height = img.shape[0]
width = img.shape[1]
# Center on screen
_, _, mw, mh = glfw.get_monitor_workarea(glfw.get_primary_monitor())
if not mw:
vmode = glfw.get_video_mode(glfw.get_primary_monitor())
mw, mh = vmode.size
wscale, hscale = glfw.get_monitor_content_scale(glfw.get_primary_monitor())
else:
wscale, hscale = 1, 1
window = glfw.create_window(int(width/wscale), int(height/hscale), "Slideflow Studio", None, None)
glfw.set_window_pos(window, (mw - int(width/wscale)) // 2, (mh - int(height/hscale)) // 2)
_tex_bg = None
_tex_icon = None
_version_text = None
_first_frame = True
if not window:
glfw.terminate()
return
glfw.make_context_current(window)
while not glfw.window_should_close(window):
glfw.poll_events()
# Initialize GL state.
gl.glViewport(0, 0, width, height)
gl.glMatrixMode(gl.GL_PROJECTION)
gl.glLoadIdentity()
gl.glTranslate(-1, 1, 0)
gl.glScale(2 / max(width, 1), -2 / max(height, 1), 1)
gl.glMatrixMode(gl.GL_MODELVIEW)
gl.glLoadIdentity()
gl.glEnable(gl.GL_BLEND)
gl.glBlendFunc(gl.GL_ONE, gl.GL_ONE_MINUS_SRC_ALPHA) # Pre-multiplied alpha.
# Clear.
gl.glClearColor(0, 0, 0, 1)
gl.glClear(gl.GL_COLOR_BUFFER_BIT | gl.GL_DEPTH_BUFFER_BIT)
if _tex_bg is None:
_tex_bg = Texture(image=img, bilinear=False)
if _tex_icon is None:
_tex_icon = Texture(image=icon, bilinear=True)
if _version_text is None:
_version_text = text_texture(__version__, size=22)
_tex_bg.draw(pos=0, zoom=1, align=0.5, rint=True, anchor='topleft')
_tex_icon.draw(pos=(width//2, int(height * 0.3)), zoom=0.25, align=0.5, rint=True, anchor='center')
_version_text.draw(pos=(width//2, int(height * 0.7)), zoom=1, align=0.5, rint=True, anchor='center')
if not _first_frame:
glfw.show_window(window)
_first_frame = False
glfw.swap_buffers(window)
if _imported:
glfw.destroy_window(window)
glfw.default_window_hints()
break
glfw.terminate()
# -----------------------------------------------------------------------------
class Texture:
"""Class to assist with creation and render of an OpenGL texture."""
_texture_formats = {
('uint8', 1): dict(type=gl.GL_UNSIGNED_BYTE, format=gl.GL_LUMINANCE, internalformat=gl.GL_LUMINANCE8),
('uint8', 2): dict(type=gl.GL_UNSIGNED_BYTE, format=gl.GL_LUMINANCE_ALPHA, internalformat=gl.GL_LUMINANCE8_ALPHA8),
('uint8', 3): dict(type=gl.GL_UNSIGNED_BYTE, format=gl.GL_RGB, internalformat=gl.GL_RGB8),
('uint8', 4): dict(type=gl.GL_UNSIGNED_BYTE, format=gl.GL_RGBA, internalformat=gl.GL_RGBA8),
('float32', 1): dict(type=gl.GL_FLOAT, format=gl.GL_LUMINANCE, internalformat=gl.ARB.texture_float.GL_LUMINANCE32F_ARB),
('float32', 2): dict(type=gl.GL_FLOAT, format=gl.GL_LUMINANCE_ALPHA, internalformat=gl.ARB.texture_float.GL_LUMINANCE_ALPHA32F_ARB),
('float32', 3): dict(type=gl.GL_FLOAT, format=gl.GL_RGB, internalformat=gl.GL_RGB32F),
('float32', 4): dict(type=gl.GL_FLOAT, format=gl.GL_RGBA, internalformat=gl.GL_RGBA32F),
}
def __init__(
self,
*,
image=None,
width=None,
height=None,
channels=None,
dtype=None,
bilinear=True,
mipmap=True
) -> None:
self.gl_id = None
self.bilinear = bilinear
self.mipmap = mipmap
# Determine size and dtype.
if image is not None:
image = np.asarray(image)
if image.ndim == 2:
image = image[:, :, np.newaxis]
if image.dtype.name == 'float64':
image = image.astype('float32')
self.height, self.width, self.channels = image.shape
self.dtype = image.dtype
else:
assert width is not None and height is not None
self.width = width
self.height = height
self.channels = channels if channels is not None else 3
self.dtype = np.dtype(dtype) if dtype is not None else np.uint8
# Validate size and dtype.
assert isinstance(self.width, int) and self.width >= 0
assert isinstance(self.height, int) and self.height >= 0
assert isinstance(self.channels, int) and self.channels >= 1
# Create texture object.
self.gl_id = gl.glGenTextures(1)
with self.bind():
gl.glTexParameterf(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_S, gl.GL_CLAMP_TO_EDGE)
gl.glTexParameterf(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_T, gl.GL_CLAMP_TO_EDGE)
gl.glTexParameterf(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MAG_FILTER, gl.GL_LINEAR if self.bilinear else gl.GL_NEAREST)
gl.glTexParameterf(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MIN_FILTER, gl.GL_LINEAR_MIPMAP_LINEAR if self.mipmap else gl.GL_NEAREST)
with self.bind():
fmt = self._texture_formats[(np.dtype(self.dtype).name, int(self.channels))]
gl.glPushClientAttrib(gl.GL_CLIENT_PIXEL_STORE_BIT)
gl.glPixelStorei(gl.GL_UNPACK_ALIGNMENT, 1)
gl.glTexImage2D(gl.GL_TEXTURE_2D, 0, fmt['internalformat'], self.width, self.height, 0, fmt['format'], fmt['type'], image)
if self.mipmap:
gl.glGenerateMipmap(gl.GL_TEXTURE_2D)
gl.glPopClientAttrib()
@contextmanager
def bind(self):
prev_id = gl.glGetInteger(gl.GL_TEXTURE_BINDING_2D)
gl.glBindTexture(gl.GL_TEXTURE_2D, self.gl_id)
yield
gl.glBindTexture(gl.GL_TEXTURE_2D, prev_id)
def draw(self, *, pos=0, zoom=1, align=0, rint=False, color=1, alpha=1, rounding=0, anchor='center'):
zoom = np.broadcast_to(np.asarray(zoom, dtype='float32'), [2])
size = zoom * [self.width, self.height]
with self.bind():
gl.glPushAttrib(gl.GL_ENABLE_BIT)
gl.glEnable(gl.GL_TEXTURE_2D)
self._draw_rect(pos=pos, size=size, align=align, rint=rint, color=color, alpha=alpha, rounding=rounding, anchor=anchor)
gl.glPopAttrib()
def delete(self):
if self.gl_id is not None:
gl.glDeleteTextures([self.gl_id])
self.gl_id = None
def __del__(self):
try:
self.delete()
except:
pass
def _draw_rect(self, *, pos=0, pos2=None, size=None, align=0, rint=False, color=1, alpha=1, rounding=0, mode=gl.GL_TRIANGLE_FAN, anchor='center'):
assert pos2 is None or size is None
assert anchor in ('center', 'topleft')
pos = np.broadcast_to(np.asarray(pos, dtype='float32'), [2])
pos2 = np.broadcast_to(np.asarray(pos2, dtype='float32'), [2]) if pos2 is not None else None
size = np.broadcast_to(np.asarray(size, dtype='float32'), [2]) if size is not None else None
size = size if size is not None else pos2 - pos if pos2 is not None else np.array([1, 1], dtype='float32')
pos = pos - size * align
if rint:
pos = np.rint(pos)
rounding = np.broadcast_to(np.asarray(rounding, dtype='float32'), [2])
rounding = np.minimum(np.abs(rounding) / np.maximum(np.abs(size), 1e-8), 0.5)
if np.min(rounding) == 0:
rounding *= 0
vertices = self._setup_center_rect(float(rounding[0]), float(rounding[1]))
self._draw_shape(vertices, pos=pos, size=size, color=color, alpha=alpha, mode=mode, anchor=anchor)
def _draw_shape(self, vertices, *, mode=gl.GL_TRIANGLE_FAN, pos=0, size=1, color=1, alpha=1, anchor='center'):
assert vertices.ndim == 2 and vertices.shape[1] == 2
assert anchor in ('center', 'topleft')
pos = np.broadcast_to(np.asarray(pos, dtype='float32'), [2])
size = np.broadcast_to(np.asarray(size, dtype='float32'), [2])
color = np.broadcast_to(np.asarray(color, dtype='float32'), [3])
alpha = np.clip(np.broadcast_to(np.asarray(alpha, dtype='float32'), []), 0, 1)
gl.glPushClientAttrib(gl.GL_CLIENT_VERTEX_ARRAY_BIT)
gl.glPushAttrib(gl.GL_CURRENT_BIT | gl.GL_TRANSFORM_BIT)
gl.glMatrixMode(gl.GL_MODELVIEW)
gl.glPushMatrix()
gl.glEnableClientState(gl.GL_VERTEX_ARRAY)
gl.glEnableClientState(gl.GL_TEXTURE_COORD_ARRAY)
gl.glVertexPointer(2, gl.GL_FLOAT, 0, vertices)
gl.glTexCoordPointer(2, gl.GL_FLOAT, 0, vertices)
if anchor == 'center':
gl.glTranslate(pos[0], pos[1], 0)
else:
gl.glTranslate(pos[0]+size[0]/2, pos[1]+size[1]/2, 0)
gl.glScale(size[0], size[1], 1)
gl.glColor4f(color[0] * alpha, color[1] * alpha, color[2] * alpha, alpha)
gl.glDrawArrays(mode, 0, vertices.shape[0])
gl.glPopMatrix()
gl.glPopAttrib()
gl.glPopClientAttrib()
@lru_cache(maxsize=10000)
def _setup_center_rect(self, rx, ry):
t = np.linspace(0, np.pi / 2, 1 if max(rx, ry) == 0 else 64)
s = 1 - np.sin(t); c = 1 - np.cos(t)
x = [c * rx, 1 - s * rx, 1 - c * rx, s * rx]
y = [s * ry, c * ry, 1 - s * ry, 1 - c * ry]
v = np.stack([x, y], axis=-1).reshape(-1, 2)
return v.astype('float32')
@lru_cache(maxsize=10000)
def _text_to_array(string, *, font=None, size=32, line_pad: int=None):
if font is None:
sf_root = pkgutil.get_loader('slideflow').get_filename()
font = join(dirname(sf_root), 'studio', 'gui', 'fonts', 'DroidSans.ttf')
pil_font = ImageFont.truetype(font=font, size=size)
lines = [pil_font.getmask(line, 'L') for line in string.split('\n')]
lines = [np.array(line, dtype=np.uint8).reshape([line.size[1], line.size[0]]) for line in lines]
width = max(line.shape[1] for line in lines)
lines = [np.pad(line, ((0, 0), (0, width - line.shape[1])), mode='constant') for line in lines]
line_spacing = line_pad if line_pad is not None else size // 2
lines = [np.pad(line, ((0, line_spacing), (0, 0)), mode='constant') for line in lines[:-1]] + lines[-1:]
mask = np.concatenate(lines, axis=0)
alpha = mask
return np.stack([mask, alpha], axis=-1)
@lru_cache(maxsize=10000)
def text_texture(string, bilinear=False, mipmap=True, **kwargs):
return Texture(image=_text_to_array(string, **kwargs), bilinear=bilinear, mipmap=mipmap)
#----------------------------------------------------------------------------
if __name__ == "__main__":
main()
#----------------------------------------------------------------------------
Datasets
Models
