compphysutils 0.4.0__tar.gz → 0.4.2__tar.gz

{compphysutils-0.4.0 → compphysutils-0.4.2}/MANIFEST.in

@@ -1,4 +1,6 @@
 include examples/cluster.cfg examples/na_pyramid_100.cfg
 include src/compphysutils/crystalgen/gencluster
 include src/compphysutils/graphics/plotconfig
+include src/compphysutils/graphics/plotcoords
+include src/compphysutils/graphics/plot3dcoords
 include src/compphysutils/parser/runparser src/compphysutils/parser/parsecoords src/compphysutils/parser/runcombine

{compphysutils-0.4.0/src/compphysutils.egg-info → compphysutils-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: compphysutils
-Version: 0.4.0
+Version: 0.4.2
 Summary: Set of utilities for computational condensed matter physics
 Home-page: https://github.com/StepanMarek/CompPhysUtils
 Author: Stepan Marek
@@ -11,6 +11,11 @@ Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: COPYING.reference
+Requires-Dist: matplotlib>=3.10.1
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: raylib>=5.5.0.0
+Dynamic: license-file
 
 # CompPhysUtils
 ## Collection of Python utilities for Computational Condensed Matter Physicists

{compphysutils-0.4.0 → compphysutils-0.4.2}/pyproject.toml

@@ -1,6 +1,5 @@
 [build-system]
 requires = [
-	"setuptools>=42",
-	"wheel"
+	"setuptools>=42"
 ]
 build-backend = "setuptools.build_meta"

{compphysutils-0.4.0 → compphysutils-0.4.2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = compphysutils
-version = 0.4.0
+version = 0.4.2
 author = Stepan Marek
 description = Set of utilities for computational condensed matter physics
 long_description = file: README.md
@@ -12,11 +12,16 @@ classifiers =
 	Development Status :: 3 - Alpha
 
 [options]
-package-dir = 
+package_dir = 
 	= src
 include_package_data = True
 packages = find:
 python_requires = >=3.6
+install_requires = 
+	matplotlib >= 3.10.1
+	numpy
+	scipy
+	raylib >= 5.5.0.0
 
 [options.packages.find]
 where = src
@@ -24,6 +29,7 @@ where = src
 [options.package_data]
 gencluster = src/compphysutils/crystalgen/gencluster
 plotconfig = src/compphysutils/graphics/plotconfig
+plot3dcoords = src/compphysutils/graphics/plot3dcoords
 
 [egg_info]
 tag_build = 

compphysutils-0.4.2/src/compphysutils/graphics/__init__.py

@@ -0,0 +1,3 @@
+from .atom_plot import atom_colors, atom_sizes
+
+__all__ = ["parser"]

compphysutils-0.4.2/src/compphysutils/graphics/atom_plot.py

@@ -0,0 +1,13 @@
+atom_colors = {
+    "H"  : [255,255,255,255],
+    "C"  : [  0,  0,  0,255],
+    "FE" : [210,120, 10,255],
+    "AU" : [255,209, 35,255]
+}
+
+atom_sizes = {
+    "H"  : 0.5,
+    "C"  : 0.7,
+    "FE" : 1.2,
+    "AU" : 1.5
+}

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/graphics/decorate/image.py

@@ -4,7 +4,7 @@ import numpy
 imageAP = argparse.ArgumentParser("Plots the image loaded as dataset to a given axis coordinate dimension.")
 imageAP.add_argument("imageDataset", help="Name of the dataset containing the RGB(A) data. They should be in an unrolled loop.")
 imageAP.add_argument("imageRect", nargs=4, type=float, help="Rectangle for the image to be drawn into, in axes coordinates. (x,y,width,height).")
-imageAP.add_argument("--shape", type=lambda x: list(map(int, x.split(","))), help="Shape of the image, in format width,height.")
+imageAP.add_argument("--shape", type=int, nargs=2, help="Shape of the image, in format width,height.")
 
 def command(axes, datasets, argString):
     args = imageAP.parse_args(argString)

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/graphics/fitter.py

@@ -86,10 +86,13 @@ def plotFit(dataset, fitFunctionName, axisObj, **fitParams):
         popt = guesses
         perr = guesses
     else:
-        if len(dataset) == 3:
-            popt, pcov = curve_fit(fitFunctions[fitFunctionName], dataset[0][ixMin:ixMax+1], dataset[1][ixMin:ixMax+1], sigma=dataset[2][ixMin:ixMax+1], p0=guesses)
-        else:
-            popt, pcov = curve_fit(fitFunctions[fitFunctionName], dataset[0][ixMin:ixMax+1], dataset[1][ixMin:ixMax+1], p0=guesses)
+        try:
+            if len(dataset) == 3:
+                popt, pcov = curve_fit(fitFunctions[fitFunctionName], dataset[0][ixMin:ixMax+1], dataset[1][ixMin:ixMax+1], sigma=dataset[2][ixMin:ixMax+1], p0=guesses)
+            else:
+                popt, pcov = curve_fit(fitFunctions[fitFunctionName], dataset[0][ixMin:ixMax+1], dataset[1][ixMin:ixMax+1], p0=guesses)
+        except RuntimeError:
+            raise RuntimeError(f'Did not manage to find params for fit {fitParams["fitIndex"]}')
         perr = []
         for i in range(len(pcov)):
             perr.append(pcov[i][i] ** 0.5)
@@ -102,9 +105,9 @@ def plotFit(dataset, fitFunctionName, axisObj, **fitParams):
         xs.append(xMin + dx*i)
         ys.append(fitFunctions[fitFunctionName](xMin + dx*i, *popt))
     if fitParams["fitLabel"]:
-        axisObj.plot(xs,ys,label=fitParams["fitLabel"],color=next(fitParams["fitColorCycle"]))
+        axisObj.plot(xs,ys,label=fitParams["fitLabel"],color=next(fitParams["fitColorCycle"]),ls=next(fitParams["fitLinestyleCycle"]))
     else:
-        axisObj.plot(xs,ys,color=next(fitParams["fitColorCycle"]))
+        axisObj.plot(xs,ys,color=next(fitParams["fitColorCycle"]),ls=next(fitParams["fitLinestyleCycle"]))
     # Construct the param string
     if fitParams["showParams"]:
         pstring = ""
@@ -118,8 +121,8 @@ def plotFit(dataset, fitFunctionName, axisObj, **fitParams):
         if fitParams["paramsPlacement"]:
             # Text anchor is the bottom left corner by default
             if fitParams["paramsPlacement"] == "tl":
-                axisObj.text(0.1, 0.9-0.05*(len(popt)-1)-0.05*(fitParams["paramsOffset"]), pstring, transform=axisObj.transAxes)
+                axisObj.text(0.1, 0.9-0.07*(len(popt)-1)-0.07*(fitParams["paramsOffset"]), pstring, transform=axisObj.transAxes)
         else:
             # Default to top left
-            axisObj.text(0.1, 0.9-0.05*(len(popt)-1)-0.05*(fitParams["paramsOffset"]), pstring, transform=axisObj.transAxes)
-    return popt
+            axisObj.text(1.1, 0.9-0.07*(len(popt)-1)-0.07*(fitParams["paramsOffset"]), pstring, transform=axisObj.transAxes)
+    return popt, perr

compphysutils-0.4.2/src/compphysutils/graphics/plot3dcoords

@@ -0,0 +1,87 @@
+#!/usr/bin/env python3
+import argparse
+from compphysutils.parser import readFile
+import pyray
+from compphysutils.graphics.atom_plot import atom_sizes, atom_colors
+import numpy
+from compphysutils.graphics.plotter import ColorIterator
+
+argparser = argparse.ArgumentParser(prog="plot3dcoords", description="Plots the coordinates and optionally isosurfaces using pyraylib.")
+argparser.add_argument("--format", "-f", dest="format", help="Name of the format of the coordinate file.")
+argparser.add_argument("--camera_pos", type=float, nargs=3, help="Initial position of the camera. Default : (0,0,10)", default=(0.0,0.0,10.0))
+argparser.add_argument("--triangles", nargs="*", default=False, help="Filenames containing column triangulation data for surfaces (isosurfaces) to be plotted.")
+argparser.add_argument("--sphere_res", default=30, type=int, help="Resolution of individual spheres - sets rings + sections. [default : 10]")
+argparser.add_argument("coordinate_file", help="Name of the coordinate file to be processed")
+argparser.add_argument("savefile", help="Name of the file into which to save the rendered coordinates")
+
+args = argparser.parse_args()
+dataset = readFile(args.coordinate_file, args.format)
+# Init window and start loading models
+pyray.init_window(1024,768, args.savefile)
+
+atom_models = []
+
+for atom_index in range(len(dataset[0])):
+    # TODO : Settable rings+sections
+    sphere_mesh = pyray.gen_mesh_sphere(atom_sizes[dataset[3][atom_index].upper()], args.sphere_res, args.sphere_res)
+    atom_models.append(pyray.load_model_from_mesh(sphere_mesh))
+
+surface_models = []
+if args.triangles:
+    for surface_index in range(len(args.triangles)):
+        triset = readFile(args.triangles[surface_index], "cols", "0 1 2 3 4 5 6 7 8")
+        vertices = numpy.zeros(9*len(triset[0]), dtype=numpy.float32)
+        for i in range(len(triset[0])):
+            for j in range(9):
+                vertices[9*i+j] = triset[j][i]
+        mesh = pyray.Mesh(3*len(triset[0]), len(triset[0]), vertices)
+        pyray.upload_mesh(mesh, True)
+        surface_models.append(pyray.load_model_from_mesh(mesh))
+
+# TODO : Allow for custom setting of surface colors
+surface_color = ColorIterator("255,0,0,120 0,0,255,120")
+
+camera = pyray.Camera3D()
+camera.position = args.camera_pos
+# TODO : Set other camera parameters from the command line
+camera.up = [0,1,0]
+camera.target = [0,0,0]
+camera.fovy = 90
+camera.projection = pyray.CAMERA_PERSPECTIVE
+
+# Models uploaded, start the render loop
+while not pyray.window_should_close():
+    pyray.begin_drawing()
+    pyray.clear_background(pyray.RAYWHITE)
+    pyray.begin_mode_3d(camera)
+    # TODO : This is more flexible, but a single model might be more performant for very large structures
+    for atom_index in range(len(dataset[0])):
+        # Draw the atom
+        pyray.draw_model(atom_models[atom_index],
+                         [dataset[0][atom_index],
+                          dataset[1][atom_index],
+                          dataset[2][atom_index]],
+                         1.0,
+                         atom_colors[dataset[3][atom_index].upper()]
+                         )
+    # Draw the surfaces
+    for surface_index in range(len(surface_models)):
+        pyray.draw_model(surface_models[surface_index],
+                         [0.0, 0.0, 0.0],
+                         1.0,
+                         list(map(int, next(surface_color))))
+    pyray.end_mode_3d()
+    pyray.end_drawing()
+    # Check for screenshot
+    if pyray.is_key_pressed(pyray.KEY_S):
+        pyray.take_screenshot(args.savefile)
+    # Updating camera
+    if pyray.is_mouse_button_down(pyray.MOUSE_BUTTON_LEFT) or pyray.get_mouse_wheel_move() != 0.0:
+        pyray.update_camera(camera, pyray.CAMERA_THIRD_PERSON)
+
+for atom_index in range(len(dataset[0])):
+    pyray.unload_model(atom_models[atom_index])
+# TODO : Fix the segfault on free
+#for surface_index in range(len(surface_models)):
+#    pyray.unload_model(surface_models[surface_index])
+pyray.close_window()

compphysutils-0.4.2/src/compphysutils/graphics/plot_types/coord.py

@@ -0,0 +1,78 @@
+import argparse
+import numpy
+import matplotlib.tri as mtri
+
+ap = argparse.ArgumentParser(description="Simple render of the atomic coordinates from a coord dataset.")
+
+ap.add_argument("--view", type=lambda x: list(map(float, x.split(","))), help="Camera position in angular coordinates in degrees (azimuthal,elevation,roll). Default : (0,0,0)", default=[0,0,0])
+
+colors = {
+    "au" : "#ffcc00",
+    "na" : "#ffff00",
+    "fe" : "#ff9933",
+    "h"  : "#ffffff",
+    "c"  : "#111111",
+    "o"  : "#ff0000",
+    "n"  : "#0000ff",
+    "s"  : "#ffeb00",
+    "mo" : "#006792"
+}
+
+radii = {
+    "au" : 1.5,
+    "na" : 1.2,
+    "fe" : 1.4,
+    "h"  : 0.5,
+    "c"  : 1.0,
+    "o"  : 1.1,
+    "n"  : 1.1,
+    "s"  : 1.3,
+    "mo" : 1.3,
+}
+
+def plotSpheres(axes3d, position=numpy.array([[0.0],[0.0],[0.0]]), elements=False):
+    # Create the mesh
+    phi = numpy.linspace(0, numpy.pi*2, 20)
+    theta = numpy.linspace(0, numpy.pi, 20)
+    theta, phi = numpy.meshgrid(theta, phi)
+    phi, theta = phi.flatten(), theta.flatten()
+    x0 = numpy.cos(phi) * numpy.sin(theta)
+    y0 = numpy.sin(phi) * numpy.sin(theta)
+    z0 = numpy.cos(theta)
+    # Add triangulation
+    tri = mtri.Triangulation(theta, phi)
+    for j in range(len(position[0])):
+        if not elements:
+            x = x0 - position[0,j]
+            y = y0 - position[1,j]
+            z = z0 - position[2,j]
+            axes3d.plot_trisurf(x, y, z, triangles=tri.triangles, edgecolor="none",linewidth=0,antialiased=False,color="b")
+        else:
+            try:
+                x = radii[elements[j].lower()] * x0 - position[0,j]
+                y = radii[elements[j].lower()] * y0 - position[1,j]
+                z = radii[elements[j].lower()] * z0 - position[2,j]
+            except KeyError:
+                x = x0 - position[0,j]
+                y = y0 - position[1,j]
+                z = z0 - position[2,j]
+            try:
+                axes3d.plot_trisurf(x, y, z, triangles=tri.triangles, edgecolor="none",linewidth=0,antialiased=False,color=colors[elements[j].lower()])
+            except KeyError:
+                axes3d.plot_trisurf(x, y, z, triangles=tri.triangles, edgecolor="none",linewidth=0,antialiased=False,color="b")
+
+
+def plot(datasets, axisObj, **plotOptions):
+    figure = plotOptions["figure"]
+    figure.clf()
+    axes = figure.add_axes((0.0,0.0,1.0,1.0),projection="3d")
+    axes.set_axis_off()
+    args = ap.parse_args(plotOptions["plotArgString"])
+    for i in range(len(datasets)):
+        #axes.scatter(datasets[i][0], datasets[i][1], datasets[i][2])
+        if len(datasets[i]) > 3:
+            plotSpheres(axes, position=numpy.array(datasets[i][0:3]), elements=datasets[i][3])
+        else:
+            plotSpheres(axes, position=numpy.array(datasets[i][0:3]))
+    axes.view_init(elev=args.view[1], azim=args.view[0], roll=args.view[2])
+    return axes

compphysutils-0.4.2/src/compphysutils/graphics/plot_types/errorbar.py

@@ -0,0 +1,47 @@
+import argparse
+
+ap = argparse.ArgumentParser(prog="errorbar", description="Plot scatter with error bounds.")
+ap.add_argument("--lineWidth", default=0, type=float, help="Width of the line joining the points. [default : 0]")
+ap.add_argument("--elineWidth", default=2, type=float, help="Width of the error bar line. [default : 2]")
+ap.add_argument("--singleErr", default="y", choices=["x", "y"], help="When only a single error set is provided, which coordinate it corresponds to.")
+
+def plot(datasets, axisObj, datasetLabels=False, **plotOptions):
+    args = ap.parse_args(plotOptions["plotArgString"])
+    if not datasetLabels:
+        datasetLabels = [None] * len(datasets)
+    for dataIndex in range(len(datasets)):
+        if len(datasets[dataIndex]) >= 4:
+            # If at least four columns provided, plot errors on both axes
+            axisObj.errorbar(datasets[dataIndex][0],
+                             datasets[dataIndex][2],
+                             xerr=datasets[dataIndex][1],
+                             yerr=datasets[dataIndex][3],
+                             capsize=4,
+                             lw=args.lineWidth,
+                             elinewidth=args.elineWidth,
+                             marker=next(plotOptions["markerstyleCycle"]),
+                             label=datasetLabels[dataIndex],
+                             color=next(plotOptions["colorCycle"]))
+        else:
+            # Otherwise, just plot one error
+            if args.singleErr == "x":
+                axisObj.errorbar(datasets[dataIndex][0],
+                                 datasets[dataIndex][1],
+                                 xerr=datasets[dataIndex][2],
+                                 capsize=4,
+                                 lw=args.lineWidth,
+                                 elinewidth=args.elineWidth,
+                                 marker=next(plotOptions["markerstyleCycle"]),
+                                 label=datasetLabels[dataIndex],
+                                 color=next(plotOptions["colorCycle"]))
+            else:
+                axisObj.errorbar(datasets[dataIndex][0],
+                                 datasets[dataIndex][1],
+                                 yerr=datasets[dataIndex][2],
+                                 capsize=4,
+                                 lw=args.lineWidth,
+                                 elinewidth=args.elineWidth,
+                                 marker=next(plotOptions["markerstyleCycle"]),
+                                 label=datasetLabels[dataIndex],
+                                 color=next(plotOptions["colorCycle"]))
+    return axisObj

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/graphics/plot_types/quiver.py

@@ -13,6 +13,10 @@ ap.add_argument("--scale", default=1, type=float, help="Scale used for the matla
 ap.add_argument("--scaleUnits", default="xy", help="Scale units used for the matlab primitive. Default : xy")
 ap.add_argument("--units", default="xy", help="Units used for the matlab primitive. Default : xy")
 ap.add_argument("--pivot", default="tail", help="Pivot used for the matlab primitive. Default : tail")
+ap.add_argument("--headlength", default=10, type=float, help="Headlength argument passed to the matlab primitive. Default : 10")
+ap.add_argument("--headwidth", default=10, type=float, help="Headlength argument passed to the matlab primitive. Default : 10")
+ap.add_argument("--headaxislength", default=10, type=float, help="Headlength argument passed to the matlab primitive. Default : 10")
+ap.add_argument("--stride", default=1, type=int, help="Optionally, stride the points in both directions to reduce the number of points.")
 
 def plot(datasets, axisObj, datasetLabels=False, **plotOptions):
     args = ap.parse_args(plotOptions["plotArgString"])
@@ -40,6 +44,15 @@ def plot(datasets, axisObj, datasetLabels=False, **plotOptions):
         if args.normalize:
             components = components / (numpy.sum(components ** 2, axis=0) ** 0.5)
         # Change default arrow style to resamble annotation arrows
+        if args.stride != 1:
+            print(coordinates.shape)
+            coordinates = numpy.lib.stride_tricks.as_strided(coordinates,
+                    shape=(coordinates.shape[0], coordinates.shape[1]//args.stride, coordinates.shape[2]//args.stride),
+                    strides=(coordinates.strides[0], coordinates.strides[1]*args.stride, coordinates.strides[2]*args.stride))
+            print(coordinates.shape)
+            components = numpy.lib.stride_tricks.as_strided(components,
+                    shape=(components.shape[0], components.shape[1]//args.stride, components.shape[2]//args.stride),
+                    strides=(components.strides[0], components.strides[1]*args.stride, components.strides[2]*args.stride))
         axisObj.quiver(*coordinates, *components,
             label=datasetLabels[datasetIndex],
             color=next(plotOptions["colorCycle"]),
@@ -48,48 +61,8 @@ def plot(datasets, axisObj, datasetLabels=False, **plotOptions):
             scale_units=args.scaleUnits,
             units=args.units,
             pivot=args.pivot,
-            headlength=10,
-            headaxislength=10,
-            headwidth=10
+            headlength=args.headlength,
+            headaxislength=args.headaxislength,
+            headwidth=args.headwidth
         )
     return axisObj
-#def plot(datasets, axisObj, datasetLabels=False, **plotOptions):
-#    # Datasets are cols,columns,rows organized
-#    if not datasetLabels:
-#        datasetLabels = [False] * len(datasets)
-#    # Parse arguments
-#    args = ap.parse_args(plotOptions["plotArgString"])
-#    # Now, determine stride
-#    if args.plane == "xy":
-#        # Keep a constant z
-#        if args.changeOrder == "xyz":
-#            # Simplest case - simply take consecutive points - equal to stride 1
-#            # Find start
-#            startIndex = args.loneIndex * args.gridsize[0] * args.gridsize[1]
-#            finalIndex = startIndex + args.gridsize[0] * args.gridsize[1]
-#            stride = 1
-#            # Extract the required fields
-#            for colIndex in range(len(datasets)):
-#                x = numpy.array(datasets[colIndex][0])
-#                y = numpy.array(datasets[colIndex][1])
-#                z = numpy.array(datasets[colIndex][2])
-#                curr_x = numpy.array(datasets[colIndex][0])
-#                curr_y = numpy.array(datasets[colIndex][1])
-#                curr_z = numpy.array(datasets[colIndex][2])
-#                x_plot = x[startIndex:finalIndex:stride]
-#                y_plot = y[startIndex:finalIndex:stride]
-#                curr_x_plot = curr_x[startIndex:finalIndex:stride]
-#                curr_y_plot = curr_y[startIndex:finalIndex:stride]
-#            # Plot the quiver
-#            zValue = z[startIndex]
-#            zValue = round(zValue, 2)
-#            axisObj.quiver(x_plot, y_plot, curr_x_plot, curr_y_plot,
-#                label="$z = "+str(zValue)+"$",
-#                color=next(plotOptions["colorCycle"]),
-#                linestyle=next(plotOptions["linestyleCycle"]),
-#                angles="xy",
-#                scale=0.3*max((max(curr_x_plot), max(curr_y_plot))),
-#                units="xy",
-#            )
-#    # Return the axis object
-#    return axisObj

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/graphics/plotconfig

@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 import argparse
 from compphysutils.graphics.plotter import fromConfig
 

compphysutils-0.4.2/src/compphysutils/graphics/plotcoords

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+import argparse
+from compphysutils.parser import readFile
+from compphysutils.graphics.plotter import plot
+import matplotlib.pyplot as plt
+
+argparser = argparse.ArgumentParser(description="Plots the coordinates, using default parameters.")
+argparser.add_argument("--format", "-f", dest="format", help="Name of the format of the coordinate file.")
+argparser.add_argument("--view", help="View option broadcasted to coord plot : Camera position in angular coordinates in degrees (azimuthal,elevation,roll). Default : (0,0,0)", default="0,0,0")
+argparser.add_argument("--dpi", default=300, type=int, help="Resolution of the coord image")
+argparser.add_argument("coordinate_file", help="Name of the coordinate file to be processed")
+argparser.add_argument("savefile", help="Name of the file into which to save the rendered coordinates")
+
+args = argparser.parse_args()
+dataset = readFile(args.coordinate_file, args.format)
+# TODO : Variable figure size?
+plt.gcf().set_size_inches(4,4)
+# TODO : Axes limits
+plot([dataset], "coord", axes=plt.gca(), figure=plt.gcf(), plotArgString=["--view", args.view], xlabel=False, ylabel=False, xlim=False, ylim=False, xticks=False, yticks=False)
+# TODO : Variable DPI
+# TODO : Redo by default config?
+plt.savefig(args.savefile, bbox_inches="tight", dpi=args.dpi)

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/graphics/plotter.py

@@ -1,7 +1,7 @@
 import matplotlib.pyplot as plt
 from .. import __user_conf_dir
 from ..parser import parseDatasetConfig
-from ..parser import save 
+from ..parser import save, writeFile
 import configparser
 from ..parser.combine import runGroupData
 from .fitter import plotFit 
@@ -71,16 +71,16 @@ def plot(datasets, plotType="scatter", axes=False, figure=False, **plotOptions):
     if not axes:
         axes = figure.gca()
     if plotType in plotTypes:
-        plotTypes[plotType](datasets, axes, figure=figure, **plotOptions)
+        axes = plotTypes[plotType](datasets, axes, figure=figure, **plotOptions)
     elif plotType in plotModules:
         # Module is present but probably not loaded
         plotModules[plotType]["spec"].loader.exec_module(plotModules[plotType]["module"])
         plotModules[plotType]["loaded"] = True
         plotTypes[plotType] = plotModules[plotType]["module"].plot
-        plotTypes[plotType](datasets, axes, figure=figure, **plotOptions)
+        axes = plotTypes[plotType](datasets, axes, figure=figure, **plotOptions)
     else:
         # Defaults to scatter
-        plotTypes["scatter"](datasets, axes, **plotOptions)
+        axes = plotTypes["scatter"](datasets, axes, **plotOptions)
     axes.set_xlabel(plotOptions["xlabel"])
     axes.set_ylabel(plotOptions["ylabel"])
     if plotOptions["xlim"]:
@@ -92,6 +92,15 @@ def plot(datasets, plotType="scatter", axes=False, figure=False, **plotOptions):
         #axes.set_xticks(plotOptions["xticks"][0], labels=plotOptions["xticks"][1])
         axes.set_xticks(plotOptions["xticks"][0])
         axes.set_xticklabels(plotOptions["xticks"][1])
+    if plotOptions["xticks-rotate"]:
+        axes.tick_params(axis="x", labelrotation=90)
+    # If requested, move ticks to top
+    axes.tick_params(axis="x",
+                     top=plotOptions["xticks-swap"],
+                     labeltop=plotOptions["xticks-swap"],
+                     bottom=not plotOptions["xticks-swap"],
+                     labelbottom=not plotOptions["xticks-swap"]
+                     )
     if plotOptions["yticks"]:
         axes.set_yticks(plotOptions["yticks"][0])
         axes.set_yticklabels(plotOptions["yticks"][1])
@@ -164,7 +173,7 @@ def fromConfig(configFileName, axes=False, figure=False, datasets={}):
             float(cfg["plot"].get("fig-width-inches", 6.4)),
             float(cfg["plot"].get("fig-height-inches", 4.8))
     )
-    plotOptions["colorCycle"] = cfg["plot"].get("colorCycle", "b")
+    plotOptions["colorCycle"] = cfg["plot"].get("colorCycle", "r g b c m y k")
     plotOptions["colorCycle"] = ColorIterator(plotOptions["colorCycle"])
     plotOptions["linestyleCycle"] = cfg["plot"].get("linestyleCycle", "solid")
     plotOptions["linestyleCycle"] = LinestyleIterator(plotOptions["linestyleCycle"])
@@ -189,6 +198,9 @@ def fromConfig(configFileName, axes=False, figure=False, datasets={}):
             plotOptions[ticksName] = datasets[plotOptions[ticksName]]
         elif cfg["plot"].get("hide-"+ticksName, False):
             plotOptions[ticksName] = [[],[]]
+        plotOptions[ticksName+"-rotate"] = cfg["plot"].get(ticksName+"-rotate", False)
+    # xticks on top if requested
+    plotOptions["xticks-swap"] = cfg["plot"].get("xticks-swap", False)
     axes = plot(chosenDatasets, graphType, axes=axes, figure=figure, **plotOptions)
     # If the axes are hidden, hide them
     if cfg["plot"].get("hide-axes", False):
@@ -208,11 +220,29 @@ def fromConfig(configFileName, axes=False, figure=False, datasets={}):
         if len(fitLabels) < numFits:
             fitLabels += [False] * (numFits - len(fitLabels))
         prevFitParams = []
+        prevFitErrors = []
+        fitParamLengths = []
+        currFitParams = []
+        currFitErrors = []
         fitColorIterator = ColorIterator(cfg["plot"].get("fit-colorCycle", "tab:blue tab:orange tab:green tab:cyan"))
+        fitLinestyleIterator = LinestyleIterator(cfg["plot"].get("fit-linestyleCycle", ":"))
+        # Ready the ranges for fits - each fit requires a separate range
+        fitXMins = [False]*numFits
+        fitXMaxs = [False]*numFits
+        providedXMins = cfg["plot"].get("fit-xmin", False)
+        providedXMaxs = cfg["plot"].get("fit-xmax", False)
+        if providedXMins:
+            providedXMins = providedXMins.split("\n")
+            for i in range(len(providedXMins)):
+                fitXMins[i] = float(providedXMins[i])
+        if providedXMaxs:
+            providedXMaxs = providedXMaxs.split("\n")
+            for i in range(len(providedXMaxs)):
+                fitXMaxs[i] = float(providedXMaxs[i])
         for allFitArgs in cfg["plot"].get("fit").split("\n"):
             fitArgs = allFitArgs.split()
             # TODO : Fit args?
-            prevFitParams += list(plotFit(
+            currFitParams, currFitErrors = plotFit(
                 chosenDatasets[int(fitArgs[1])],
                 fitArgs[0],
                 axes,
@@ -221,13 +251,45 @@ def fromConfig(configFileName, axes=False, figure=False, datasets={}):
                 showParams=cfg["plot"].getboolean("fit-show-params", True),
                 showError=cfg["plot"].getboolean("fit-show-error", True),
                 fitColorCycle=fitColorIterator,
+                fitLinestyleCycle=fitLinestyleIterator,
                 paramsPlacement=cfg["plot"].get("params-placement", False),
                 paramsOffset=len(prevFitParams),
-                xMin=float(cfg["plot"].get("fit-xmin", False)),
-                xMax=float(cfg["plot"].get("fit-xmax", False)),
-                dirtyRun=cfg["plot"].getboolean("fit-dirty-run", False)
-                ))
+                xMin=fitXMins[fitIndex],
+                xMax=fitXMaxs[fitIndex],
+                dirtyRun=cfg["plot"].getboolean("fit-dirty-run", False),
+                fitIndex=fitIndex
+                )
             fitIndex += 1
+            prevFitParams += list(currFitParams)
+            prevFitErrors += list(currFitErrors)
+            fitParamLengths.append(len(currFitParams))
+        # Save fit params, if required
+        fitSaveName = cfg["plot"].get("fit-savepoint", False)
+        if fitSaveName:
+            fitSaveArgs = fitSaveName.split()
+            # No context name nor dataset name, only format and target filename (optional)
+            fitFormatName = fitSaveArgs[0]
+            fitFileName = "fit.dat"
+            fitParserArgs = False
+            if len(fitSaveArgs) > 1:
+                fitFileName = fitSaveArgs[1]
+            if len(fitSaveArgs) > 2:
+                fitParserArgs = " ".join(fitSaveArgs[2:])
+            # Regularize to dataset - take the first fit as determination
+            dataset = []
+            for j in range(fitParamLengths[0]):
+                dataset.append([])
+                # Append for both value and error
+                dataset.append([])
+            fitNumCols = fitParamLengths[0]
+            paramOffset = 0
+            for i in range(len(fitParamLengths)):
+                for j in range(fitNumCols):
+                    dataset[2*j].append(prevFitParams[paramOffset + j])
+                    dataset[2*j+1].append(prevFitErrors[paramOffset + j])
+                paramOffset += fitParamLengths[i]
+            # Dataset regularized, output
+            writeFile(fitFileName, fitFormatName, dataset, fitParserArgs)
     # Handle decorations for main axes
     if cfg["plot"].get("decorate", False):
         decorationCommands = cfg["plot"].get("decorate").split("\n")
@@ -298,6 +360,9 @@ def fromConfig(configFileName, axes=False, figure=False, datasets={}):
         # Plot another dataset sharing the same x axis but different y axis
         # Always, only a single twinx makes sense - provide no arguments
         fromConfig(cfg["plot"].get("twinx"), axes=axes.twinx(), figure=figure, datasets=datasets)
+    if cfg["plot"].get("twiny", False):
+        # same as twinx, but for shared y-axis
+        fromConfig(cfg["plot"].get("twiny"), axes=axes.twiny(), figure=figure, datasets=datasets)
     # If axes are provided, assume figure is printed somewhere else
     # TODO : Is this a reasonable assumption?
     if axesGiven:

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/__init__.py

@@ -1 +1 @@
-from .parser import parseDatasetConfig, save, writeFile, readFile
+from .parser import parseDatasetConfig, save, writeFile, readFile, parseRange

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/combine_commands/average.py

@@ -1,6 +1,6 @@
 import argparse
 
-averageAP = argparse.ArgumentParser()
+averageAP = argparse.ArgumentParser(prog="average", help="Element-wise average of the columns")
 averageAP.add_argument("--stderr", action="store_true", help="If given, second column of the new dataset includes standard error given by the average. Need at least two averaging datasets.")
 averageAP.add_argument("new_name", help="Name of the dataset containing the averaged values.")
 averageAP.add_argument("datasets_to_average", nargs="+", help="Datasets that are to be averaged, elementwise in each column. Number of columns is given by the first dataset.")

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/combine_commands/union.py

@@ -10,6 +10,6 @@ def command(datasets, commandArgs):
     for i in range(ncols):
         newcols.append([])
         for datasetName in args.datasets_to_merge:
-            newcols[i] = newcols[i] + datasets[datasetName][i]
+            newcols[i] = newcols[i] + list(datasets[datasetName][i])
     datasets[args.new_name] = newcols
     return datasets

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/parsecoords

@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 import argparse
 import sys
 from compphysutils.parser import writeFile, readFile

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/parser.py

@@ -287,3 +287,30 @@ def parseDatasetConfig(configFilename):
             if "savepoint" in cfg[groupName]:
                 save(cfg[groupName].get("savepoint"), "post-process", datasets, datasetName)
     return datasets
+
+def parseRange(rangeString):
+    """
+    A helper routine that parses the python-like range to array of bounds.
+    Typical behaviour is
+
+    ':' -> [0,-1]
+    '10:' -> [10,-1]
+    ':20' -> [0,19]
+    '1:5' -> [1,4]
+
+    As a special case, also handles single element access
+
+    '5' -> [5]
+    """
+    splitRange = rangeString.split(":")
+    if len(splitRange) == 1:
+        return [int(splitRange[0])]
+    elif len(splitRange) == 2:
+        toReturn = [0,-1]
+        if splitRange[0] != "":
+            toReturn[0] = int(splitRange[0])
+        if splitRange[1] != "":
+            toReturn[1] = int(splitRange[1])
+        return toReturn
+    else:
+        raise ValueError("Cannot parse "+rangeString+" as python-like range.")

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/parsers/cols.py

@@ -6,15 +6,24 @@ class ColsReference:
     def __init__(self, parserArgs=["0"]):
         self.argsReader = argparse.ArgumentParser(description="Parses the arguments for the parser itself.")
         self.argsReader.add_argument("--comment", help="Character to be used as indicator of comment. [default : #]", default="#")
+        self.argsReader.add_argument("--skip", type=int, default=0, help="Skip a given number of lines before starting the read.")
         self.argsReader.add_argument("cols", nargs="+", type=int, help="Indices of columns to read.")
         self.args = self.argsReader.parse_args(parserArgs)
+        self.skips_remaining = self.args.skip
 
     def continueReading(self, line):
-        if line[0] == self.args.comment:
+        stripLine = line.strip()
+        if self.skips_remaining > 0:
+            self.skips_remaining -= 1
+            return False
+        if len(stripLine) == 0:
+            # Do not attempt to read empty lines
+            return False
+        if stripLine[0] == self.args.comment:
             return False
         # Not commented, read
         # TODO : Different var types
-        splitLine = line.split()
+        splitLine = stripLine.split()
         retVal = []
         for i in self.args.cols:
             retVal.append(float(splitLine[i]))

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/post_processor.py

@@ -1,6 +1,6 @@
 import os
 from .. import __user_conf_dir
-import importlib
+import importlib.util
 
 ## Search for default post-processing commands
 roots = []

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/runcombine

@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 import argparse
 import sys
 import configparser

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils/parser/runparser

@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 import argparse
 import sys
 from compphysutils.parser import parseDatasetConfig

{compphysutils-0.4.0 → compphysutils-0.4.2/src/compphysutils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: compphysutils
-Version: 0.4.0
+Version: 0.4.2
 Summary: Set of utilities for computational condensed matter physics
 Home-page: https://github.com/StepanMarek/CompPhysUtils
 Author: Stepan Marek
@@ -11,6 +11,11 @@ Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: COPYING.reference
+Requires-Dist: matplotlib>=3.10.1
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: raylib>=5.5.0.0
+Dynamic: license-file
 
 # CompPhysUtils
 ## Collection of Python utilities for Computational Condensed Matter Physicists

{compphysutils-0.4.0 → compphysutils-0.4.2}/src/compphysutils.egg-info/SOURCES.txt

@@ -10,6 +10,7 @@ src/compphysutils/__init__.py
 src/compphysutils.egg-info/PKG-INFO
 src/compphysutils.egg-info/SOURCES.txt
 src/compphysutils.egg-info/dependency_links.txt
+src/compphysutils.egg-info/requires.txt
 src/compphysutils.egg-info/top_level.txt
 src/compphysutils/crystalgen/Vector.py
 src/compphysutils/crystalgen/VectorReal.py
@@ -19,9 +20,12 @@ src/compphysutils/crystalgen/gencluster
 src/compphysutils/crystalgen/generator.py
 src/compphysutils/crystalgen/readCrystalChar.py
 src/compphysutils/graphics/__init__.py
+src/compphysutils/graphics/atom_plot.py
 src/compphysutils/graphics/decorator.py
 src/compphysutils/graphics/fitter.py
+src/compphysutils/graphics/plot3dcoords
 src/compphysutils/graphics/plotconfig
+src/compphysutils/graphics/plotcoords
 src/compphysutils/graphics/plotter.py
 src/compphysutils/graphics/transformer.py
 src/compphysutils/graphics/decorate/__init__.py
@@ -37,6 +41,7 @@ src/compphysutils/graphics/fit_types/lorentz_peak.py
 src/compphysutils/graphics/fit_types/quadratic.py
 src/compphysutils/graphics/plot_types/__init__.py
 src/compphysutils/graphics/plot_types/colormap.py
+src/compphysutils/graphics/plot_types/coord.py
 src/compphysutils/graphics/plot_types/errorbar.py
 src/compphysutils/graphics/plot_types/fill_between.py
 src/compphysutils/graphics/plot_types/level.py

compphysutils-0.4.2/src/compphysutils.egg-info/requires.txt

@@ -0,0 +1,4 @@
+matplotlib>=3.10.1
+numpy
+scipy
+raylib>=5.5.0.0

compphysutils-0.4.0/src/compphysutils/graphics/__init__.py

@@ -1 +0,0 @@
-__all__ = ["parser"]

compphysutils-0.4.0/src/compphysutils/graphics/plot_types/errorbar.py

@@ -1,11 +0,0 @@
-def plot(datasets, axisObj, datasetLabels=False, **plotOptions):
-    if not datasetLabels:
-        datasetLabels = [None] * len(datasets)
-    for dataIndex in range(len(datasets)):
-        if len(datasets[dataIndex]) >= 4:
-            # If at least four columns provided, plot errors on both axes
-            axisObj.errorbar(datasets[dataIndex][0], datasets[dataIndex][2], xerr=datasets[dataIndex][1], yerr=datasets[dataIndex][3], capsize=4, lw=0, elinewidth=2, marker="p", ms=1, label=datasetLabels[dataIndex], color=next(plotOptions["colorCycle"]))
-        else:
-            # Otherwise, just plot yerr
-            axisObj.errorbar(datasets[dataIndex][0], datasets[dataIndex][1], yerr=datasets[dataIndex][2], capsize=4, lw=0, elinewidth=2, marker="p", ms=2, label=datasetLabels[dataIndex], color=next(plotOptions["colorCycle"]))
-    return axisObj