wip

axi/device.py

@@ -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)
+        bar = Bar(drawing.length, enabled=progress)
-        for path in bar(drawing.paths):
+        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):

axi/drawing.py

@@ -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])

axi/paths.py

@@ -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
+    hull = ConvexHull(points)
-    if isinstance(hull, geometry.Polygon):
+    vertices = set(i for v in hull.vertices for i in v)
-        return list(hull.exterior.coords)
+    return [hull.points[i] for i in vertices]
-    if isinstance(hull, geometry.LineString):
-        return list(hull.coords)
-    if isinstance(hull, geometry.Point):
-        return list(hull.coords)
-    raise Exception('unhandled convex hull geometry')
 
 def quadratic_path(x0, y0, x1, y1, x2, y2):
     n = int(hypot(x1 - x0, y1 - y0) + hypot(x2 - x1, y2 - y1))

axi/progress.py

@@ -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:

examples/isolines.py

@@ -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()
+    prepare()
-    main()
+    # main()

examples/paths.py

@@ -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'
+    # print 'joining paths'
-    d = d.join_paths(0.001)
+    # 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__':

examples/ribbon.py

@@ -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"
+    "Beta Subunit of the 20S Proteasome from T. acidophilum"
-, 40)
+, 36)
 
-ABSTRACT = textwrap.wrap(
+SUBTITLE = 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."
+    "These coordinates are from the 1995 crystal structure by Lowe et al. (Lowe et al., 1995). PDB entry 1PMA."
-, 120)
+    # "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():
+def subtitle():
-    ds = [axi.Drawing(p) for p in axi.justify_text(ABSTRACT, axi.TIMESR)]
+    # 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 = stack_drawings([title(), subtitle()], 0.3125)
-    text = title()
+    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 = stack_drawings([d, text], 1)
-    d = d.rotate(-90)
+    # 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')

requirements.txt

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