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This commit is contained in:
Michael Fogleman 2018-02-19 17:12:10 -05:00
parent 82c01ff78c
commit 61d82dbdc8
8 changed files with 86 additions and 43 deletions
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11
axi/device.py
View File

@ -6,10 +6,11 @@ from math import modf
from serial import Serial
from serial.tools.list_ports import comports
from .paths import path_length
from .planner import Planner
from .progress import Bar
TIMESLICE_MS = 10
TIMESLICE_MS = 20
MICROSTEPPING_MODE = 2
STEP_DIVIDER = 2 ** (MICROSTEPPING_MODE - 1)
@ -27,7 +28,7 @@ PEN_DOWN_DELAY = 0
ACCELERATION = 8
MAX_VELOCITY = 4
CORNER_FACTOR = 0.005
CORNER_FACTOR = 0.0025
VID_PID = '04D8:FD92'
@ -160,13 +161,15 @@ class Device(object):
def run_drawing(self, drawing, progress=True):
self.pen_up()
position = (0, 0)
bar = Bar(enabled=progress)
for path in bar(drawing.paths):
bar = Bar(drawing.length, enabled=progress)
for path in drawing.paths:
self.run_path([position, path[0]])
self.pen_down()
self.run_path(path)
self.pen_up()
position = path[-1]
bar.increment(path_length(path))
bar.done()
self.run_path([position, (0, 0)])
def plan_drawing(self, drawing):

21
axi/drawing.py
View File

@ -4,7 +4,7 @@ from math import sin, cos, radians
from .paths import (
simplify_paths, sort_paths, join_paths, crop_paths, convex_hull,
expand_quadratics)
expand_quadratics, paths_length)
try:
import cairo
@ -14,7 +14,12 @@ except ImportError:
class Drawing(object):
def __init__(self, paths=None):
self.paths = paths or []
self.dirty()
def dirty(self):
self._bounds = None
self._length = None
self._hull = None
@classmethod
def loads(cls, data):
@ -70,11 +75,13 @@ class Drawing(object):
@property
def convex_hull(self):
return convex_hull(self.points)
if self._hull is None:
self._hull = convex_hull(self.points)
return self._hull
@property
def bounds(self):
if not self._bounds:
if self._bounds is None:
points = self.points
if points:
x1 = min(x for x, y in points)
@ -86,6 +93,12 @@ class Drawing(object):
self._bounds = (x1, y1, x2, y2)
return self._bounds
@property
def length(self):
if self._length is None:
self._length = paths_length(self.paths)
return self._length
@property
def width(self):
x1, y1, x2, y2 = self.bounds
@ -124,7 +137,7 @@ class Drawing(object):
def add(self, drawing):
self.paths.extend(drawing.paths)
self._bounds = None
self.dirty()
def transform(self, func):
return Drawing([[func(x, y) for x, y in path] for path in self.paths])

21
axi/paths.py
View File

@ -1,4 +1,5 @@
from math import hypot
from pyhull.convex_hull import ConvexHull
from shapely import geometry
from .spatial import Index
@ -14,6 +15,15 @@ def load_paths(filename):
paths.append(path)
return paths
def path_length(points):
result = 0
for (x1, y1), (x2, y2) in zip(points, points[1:]):
result += hypot(x2 - x1, y2 - y1)
return result
def paths_length(paths):
return sum([path_length(path) for path in paths], 0)
def simplify_path(points, tolerance):
if len(points) < 2:
return points
@ -111,14 +121,9 @@ def crop_paths(paths, x1, y1, x2, y2):
return result
def convex_hull(points):
hull = geometry.MultiPoint(points).convex_hull
if isinstance(hull, geometry.Polygon):
return list(hull.exterior.coords)
if isinstance(hull, geometry.LineString):
return list(hull.coords)
if isinstance(hull, geometry.Point):
return list(hull.coords)
raise Exception('unhandled convex hull geometry')
hull = ConvexHull(points)
vertices = set(i for v in hull.vertices for i in v)
return [hull.points[i] for i in vertices]
def quadratic_path(x0, y0, x1, y1, x2, y2):
n = int(hypot(x1 - x0, y1 - y0) + hypot(x2 - x1, y2 - y1))

3
axi/progress.py
View File

@ -46,6 +46,9 @@ class Bar(object):
def __exit__(self, exc_type, exc_val, exc_tb):
self.stop()
def increment(self, delta):
self.update(self.value + delta)
def update(self, value):
self.value = value
if self.enabled:

6
examples/isolines.py
View File

@ -16,7 +16,7 @@ def prepare():
print 'rendering'
im = d.render(
scale=109 * 1, line_width=0.3/25.4,
)#show_axi_bounds=False, use_axi_bounds=False)
show_axi_bounds=False, use_axi_bounds=False)
im.write_to_png('isolines.png')
d.dump('isolines.axi')
@ -53,5 +53,5 @@ def main():
d.dump('out.axi')
if __name__ == '__main__':
# prepare()
main()
prepare()
# main()

14
examples/paths.py
View File

@ -4,22 +4,28 @@ import sys
def main():
filename = sys.argv[1]
print 'loading paths'
d = axi.Drawing(axi.load_paths(filename))
# d = axi.Drawing(axi.load_paths(filename))
d = axi.Drawing.load(filename)
print len(d.paths)
# print 'eliminating duplicate paths'
# d.paths = list(set([tuple(x) for x in d.paths]))
print 'joining paths'
d = d.join_paths(0.001)
# print 'joining paths'
# d = d.join_paths(0.001)
# print len(d.paths)
print 'transforming paths'
d = d.scale(1, -1)
# d = d.scale(1, -1)
d = d.rotate(180)
d = d.rotate_and_scale_to_fit(12, 8.5, step=90)
print 'sorting paths'
d = d.sort_paths()
print 'joining paths'
d = d.join_paths(0.01)
print len(d.paths)
print 'simplifying paths'
d = d.simplify_paths(0.001)
print 'rendering paths'
d.render(line_width=0.25/25.4).write_to_png('out.png')
d.dump('out.axi')
# axi.draw(d)
if __name__ == '__main__':

48
examples/ribbon.py
View File

@ -2,16 +2,17 @@ import axi
import sys
import textwrap
NUMBER = 'XX'
NUMBER = '34'
LABEL = '#%s' % NUMBER
TITLE = textwrap.wrap(
"X-ray structure of human beta3beta3 alcohol dehydrogenase"
, 40)
"Beta Subunit of the 20S Proteasome from T. acidophilum"
, 36)
ABSTRACT = textwrap.wrap(
"The three-dimensional structure of the human beta3beta3 dimeric alcohol dehydrogenase (beta3) was determined to 2.4-A resolution. beta3 was crystallized as a ternary complex with the coenzyme NAD+ and the competitive inhibitor 4-iodopyrazole. beta3 is a polymorphic variant at ADH2 that differs from beta1 by a single amino acid substitution of Arg-369 --> Cys. The available x-ray structures of mammalian alcohol dehydrogenases show that the side chain of Arg-369 forms an ion pair with the NAD(H) pyrophosphate to stabilize the E.NAD(H) complex. The Cys-369 side chain of beta3 cannot form this interaction. The three-dimensional structures of beta3 and beta1 are virtually identical, with the exception that Cys-369 and two water molecules in beta3 occupy the position of Arg-369 in beta1. The two waters occupy the same positions as two guanidino nitrogens of Arg-369. Hence, the number of hydrogen bonding interactions between the enzyme and NAD(H) are the same for both isoenzymes. However, beta3 differs from beta1 by the loss of the electrostatic interaction between the NAD(H) pyrophosphate and the Arg-369 side chain. The equilibrium dissociation constants of beta3 for NAD+ and NADH are 350-fold and 4000-fold higher, respectively, than those for beta1. These changes correspond to binding free energy differences of 3.5 kcal/mol for NAD+ and 4.9 kcal/mol for NADH. Thus, the Arg-369 --> Cys substitution of beta3 isoenzyme destabilizes the interaction between coenzyme and beta3 alcohol dehydrogenase."
, 120)
SUBTITLE = textwrap.wrap(
"These coordinates are from the 1995 crystal structure by Lowe et al. (Lowe et al., 1995). PDB entry 1PMA."
# "Coordinates from the 1995 crystal structure by Lowe et al. PDB entry 1PMA."
, 60)
def concat(ds):
result = axi.Drawing()
@ -46,16 +47,21 @@ def title():
spacing = max(d.height for d in ds) * 1.5
ds = [d.translate(-d.width / 2, i * spacing) for i, d in enumerate(ds)]
d = concat(ds)
d = d.scale_to_fit_width(8.5)
d = d.scale_to_fit_width(8.5 * 4 / 5)
d = d.scale_to_fit_height(0.8)
d = d.join_paths(0.01)
return d
def abstract():
ds = [axi.Drawing(p) for p in axi.justify_text(ABSTRACT, axi.TIMESR)]
def subtitle():
# ds = [axi.Drawing(p) for p in axi.justify_text(SUBTITLE, axi.TIMESR)]
# spacing = max(d.height for d in ds) * 1.5
# ds = [d.translate(0, i * spacing) for i, d in enumerate(ds)]
ds = [axi.Drawing(axi.text(line, axi.TIMESR)) for line in SUBTITLE]
spacing = max(d.height for d in ds) * 1.5
ds = [d.translate(0, i * spacing) for i, d in enumerate(ds)]
ds = [d.translate(-d.width / 2, i * spacing) for i, d in enumerate(ds)]
d = concat(ds)
d = d.scale_to_fit_width(8.5)
d = d.scale_to_fit_width(8.5 * 2 / 3)
d = d.scale_to_fit_height(0.4)
d = d.join_paths(0.01)
return d
@ -68,8 +74,10 @@ def label():
return d
def main():
# text = stack_drawings([title(), abstract()], 0.25)
text = title()
text = stack_drawings([title(), subtitle()], 0.3125)
text = text.rotate(-90)
text = text.move(12, 8.5 / 2, 1, 0.5)
# text = title()
filenames = [
sys.argv[1],
@ -83,7 +91,7 @@ def main():
print 'loading paths'
ds = []
for filename, angle in zip(filenames, angles):
ds.append(axi.Drawing(axi.load_paths(filename)).scale_to_fit(8.5, 12).scale(1, -1))
ds.append(axi.Drawing(axi.load_paths(filename)).scale(1, -1))
# d = grid_drawings(ds, 2, 1)
d = ds[0]
print len(d.paths)
@ -92,7 +100,8 @@ def main():
print len(d.paths)
print 'transforming paths'
# d = d.scale(1, -1)
d = d.rotate_and_scale_to_fit(8.5, 12 - text.height - 0.75)
d = d.rotate(180)
d = d.rotate_and_scale_to_fit(8.5, 12 - text.height)
# d = d.origin()
print 'sorting paths'
d = d.sort_paths()
@ -103,12 +112,13 @@ def main():
d = d.simplify_paths(0.001)
# add title and label and fit to page
d = stack_drawings([d, text], 0.75)
d = d.rotate(-90)
# d = stack_drawings([d, text], 1)
# d = d.rotate(-90)
# d = d.center(12, 8.5)
d = d.scale_to_fit(12, 8.5)
d = d.rotate_and_scale_to_fit(12, 8.5).translate(-text.width * 0.6666, 0)
d.add(text)
# d.add(title())
# d.add(label())
d.add(label())
print 'rendering paths'
d.render(line_width=0.25/25.4).write_to_png('out.png')

5
requirements.txt
View File

@ -1 +1,4 @@
pyserial==3.2.1
pyserial
pyhull
Shapely