Small fixes for diagrams and simulations

.gitignore

@@ -8,5 +8,4 @@ src/packsim.c
 *.so
 *.json
 
-figures/
+squish_output/
-simulations/

src/squish/common.py

@@ -142,7 +142,7 @@ class Simulation:
 
 	def add_frame(self, points: Optional[numpy.ndarray]) -> None:
 		if points is None:
-			points = np.random.random_sample((self.domain.n, 2))
+			points = np.random.random_sample((self.domain.n, 2)) * self.domain.dim
 		else:
 			if points.shape[1] != 2 or len(points.shape) > 2:
 				raise ValueError("Sites should be 2 dimensional!")

src/squish/diagram.py

@@ -8,7 +8,7 @@ from multiprocessing import Pool, cpu_count
 
 from .common import DomainParams
 
-SYMM = np.array([[1,0], [1,1], [0,1], [-1,1], [-1,0], [-1,-1], [0,-1], [1,-1]])
+SYMM = np.array([[0,0], [1,0], [1,1], [0,1], [-1,1], [-1,0], [-1,-1], [0,-1], [1,-1]])
 
 class SimData:
 	"""Stores diagram information for a simulation.
@@ -54,7 +54,7 @@ class SimData:
 			Tuple[numpy.ndarray, numpy.ndarray]: the histogram and its bins.
 
 		"""
-		if cumulative:
+		if cumul:
 			values = np.concatenate([f[stat] for f in self.stats[:(i+1)]])
 		else:
 			values = self.stats[i][stat]
@@ -70,7 +70,7 @@ class SimData:
 		hist, bin_edges = np.histogram(values, bins=bins, range=bounds)
 		bin_list = np.array([(bin_edges[i] + bin_edges[i+1])/2 for i in range(len(bin_edges)-1)])
 
-		if avg and cumulative:
+		if avg and cumul:
 			return hist / (i+1), bin_list
 
 		return hist, bin_list
@@ -122,7 +122,7 @@ class Diagram:
 
 	def voronoi_plot(self, i: int, ax: AxesSubplot) -> None:
 		domain = self.sim.domains[i]
-		n,w,h = domain.n, domain.w, domain.h
+		n, w, h = domain.n, domain.w, domain.h
 		scale = 1.5
 		area = n <= 60
 
@@ -138,14 +138,27 @@ class Diagram:
 
 		props = dict(boxstyle='round', facecolor='wheat', alpha=0.8)
 
-		if area:
+		defects = {5: {"x": [], "y": []}, 7: {"x": [], "y": []}}
-			global SYMM
+
-			for j in range(n):
+		for j in range(n):
-				for s in np.concatenate(([[0,0]], SYMM)):
+			for s in SYMM:
-					txt = ax.text(*(self.sim.voronois[i].points[j] + s*self.sim.domains[i].dim),
+				vec = (self.sim.voronois[i].points[j] + s*self.sim.domains[i].dim)
-									str(round(self.sim.stats[i]["site_areas"][j], 3)))
+
+				if area:
+					txt = ax.text(*vec, str(round(self.sim.stats[i]["site_areas"][j], 3)))
 					txt.set_clip_on(True)
 
+				if self.sim.stats[i]["site_edge_count"][j] == 5:
+					defects[5]["x"].append(vec[0])
+					defects[5]["y"].append(vec[1])
+				elif self.sim.stats[i]["site_edge_count"][j] == 7:
+					defects[7]["x"].append(vec[0])
+					defects[7]["y"].append(vec[1])
+
+		ax.scatter(defects[5]["x"], defects[5]["y"], marker="p", color="red")
+		ax.scatter(defects[7]["x"], defects[7]["y"], marker="*", color="red")
+
+
 		ax.text(0.05, 0.95, f'Energy: {self.sim.energies[i]}', transform=ax.transAxes, fontsize=14,
 				verticalalignment='top', bbox=props)
 
@@ -208,7 +221,7 @@ class Diagram:
 
 
 	def site_energies_plot(self, i: int, ax: AxesSubplot) -> None:
-		y, x = self.sim.hist("site_energies", i, self.cumulative, avg=True)
+		y, x = self.sim.hist("site_energies", i, cumul=self.cumulative, avg=True)
 
 		ax.bar(x, y, width=0.8*(x[1]-x[0]))
 		ax.title.set_text('Site Energies')
@@ -220,7 +233,7 @@ class Diagram:
 
 
 	def avg_radius_plot(self, i: int, ax: AxesSubplot) -> None:
-		y, x = self.sim.hist("avg_radius", i, self.cumulative, avg=True)
+		y, x = self.sim.hist("avg_radius", i, cumul=self.cumulative, avg=True)
 
 		ax.bar(x, y, width=0.8*(x[1]-x[0]))
 		ax.title.set_text('Site Average Radii')
@@ -232,7 +245,7 @@ class Diagram:
 
 
 	def isoparam_avg_plot(self, i: int, ax: AxesSubplot) -> None:
-		y, x = self.sim.hist("isoparam_avg", i, self.cumulative, avg=True)
+		y, x = self.sim.hist("isoparam_avg", i, cumul=self.cumulative, avg=True)
 
 		ax.bar(x,y, width=0.8*(x[1]-x[0]))
 		ax.title.set_text('Site Isoperimetric Averages')
@@ -261,9 +274,13 @@ class Diagram:
 
 
 	def eigs_plot(self, i: int, ax: AxesSubplot) -> None:
-		eigs = self.sim.stats[i]["eigs"]
+		try:
-		ax.plot(list(range(len(eigs))), eigs, marker='o', linestyle='dashed', color='C0')
+			eigs = self.sim.stats[i]["eigs"]
-		ax.plot([0,len(eigs)], [0, 0], color="red")
+			ax.plot(list(range(len(eigs))), eigs, marker='o', linestyle='dashed', color='C0')
+			ax.plot([0,len(eigs)], [0, 0], color="red")
+		except KeyError:
+			ax.text(0.5, 0.5, "Not Computed")
+
 		ax.title.set_text('Hessian Eigenvalues')
 		ax.set_xlabel("")
 		ax.set_ylabel("Value")
@@ -272,7 +289,6 @@ class Diagram:
 	def render_frames(self, frames: List[int], fol: str = 'frames') -> None:
 		(self.sim.path / fol).mkdir(exist_ok=True)
 		combo_list = []
-		print(cpu_count())
 		for i in range(cpu_count()):
 			combo_list.append((self, frames[:int((i+1)*len(frames)/cpu_count())],
 								fol, len(frames)))
@@ -281,14 +297,8 @@ class Diagram:
 			for _ in pool.imap_unordered(render_frame_range, combo_list):
 				pass
 
-		# for i, frame in enumerate(frames):
-		# 	self.generate_frame(frame, "save", fol)
-		# 	hashes = int(21*i/len(frames))
-		# 	print(f'Generating frames... |{"#"*hashes}{" "*(20-hashes)}|' + \
-		# 			f' {i+1}/{len(frames)} frames rendered.', flush=True, end='\r')
-
 		print(flush=True)
-
+		print(f'Wrote to \"{self.sim.path / fol}\".', flush=True)
 
 	def render_video(self, time: int, mode: str) -> None:
 		if mode not in ["use_all", "sample"]:

src/squish/simulation.py

@@ -198,7 +198,7 @@ class Shrink(Simulation):
 					name: Optional[str] = None) -> None:
 		super().__init__(domain, energy, name=name)
 		self.step_size, self.thres, self.accel = step_size, thres, accel
-		self.delta, self.stop_width = self.domain.w*delta, self.domain.w*stop_width
+		self.delta, self.stop_width = self.domain.w*delta/100, self.domain.w*stop_width
 
 
 	@property
@@ -208,8 +208,8 @@ class Shrink(Simulation):
 			"step_size": self.step_size,
 			"thres": self.thres,
 			"accel": self.accel,
-			"kernel_step": self.kernel_step,
+			"delta": self.delta,
-			"count": self.count
+			"stop_width": self.stop_width
 		}
 		return info
 
@@ -225,9 +225,11 @@ class Shrink(Simulation):
 			new_sites = None
 
 		width = self.domain.w
+		i = 0
 		while width >= self.stop_width:
 			# Get to equilibrium.
-			sim = Flow(self.domain, self.energy, self.thres, self.step_size, self.accel)
+			new_domain = DomainParams(self.domain.n, width, self.domain.h, self.domain.r)
+			sim = Flow(new_domain, self.energy, self.thres, self.step_size, self.accel)
 			sim.add_frame(new_sites)
 			sim.run(False, log, log_steps)
 			new_sites = sim[-1].site_arr
@@ -235,6 +237,7 @@ class Shrink(Simulation):
 			self.frames.append(sim[-1])
 			if save: self.save(self.frame_data(i))
 
-			if log: print(f'Width: {self.w:.4f}\n')
+			if log: print(f'Width: {width:.4f}\n')
 
 			width -= self.delta
+			i += 1

src/squish/squish.py

@@ -148,7 +148,7 @@ def config_sim(args):
 	if save_diagram:
 		diagram = Diagram(sim, dia_params["figures"])
 		if dia_params["filetype"] == "img":
-			diagram.render_frames()
+			diagram.render_frames(range(len(sim)))
 		elif dia_params["filetype"] == "mp4":
 			if mode == "flow":
 				diagram.render_video(dia_params["time"], "sample")