updating readin of data from notebooks + colorbars

.gitignore

@@ -1,5 +1,5 @@
 userSettings.txt
-
+Model
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

docs/src/1_examples/0_creating_sliceFigures/3_SliceLine Animations.ipynb

@@ -142,7 +142,7 @@
     "ax[0].set_aspect('equal')\n",
     "ax[0].set_facecolor('k')\n",
     "\n",
-    "ax[0].pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot[\"rho\"]+1e-99), cmap=plt.cm.get_cmap('inferno'), vmin=-17, vmax = -14)\n",
+    "ax[0].pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot[\"rho\"]+1e-99), cmap=plt.colormaps['inferno'], vmin=-17, vmax = -14)\n",
     "ax[0].set_xlim(x[0]/cgs.au, x[-1]/cgs.au)\n",
     "ax[0].set_ylim(y[0]/cgs.au, y[-1]/cgs.au)\n",
     "\n",

docs/src/1_examples/0_creating_sliceFigures/4_SlicePlot Animations.ipynb

@@ -131,7 +131,7 @@
     "Z    = np.zeros_like(X)\n",
     "smooth_rot = sk.smoothMesh(X, Y, Z, dumpData, ['rho'])\n",
     "\n",
-    "mesh = ax.pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot[\"rho\"]+1e-99), cmap=plt.cm.get_cmap('inferno'), vmin=-17, vmax = -14)\n",
+    "mesh = ax.pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot[\"rho\"]+1e-99), cmap=plt.colormaps['inferno'], vmin=-17, vmax = -14)\n",
     "ax.set_xlim(x[0]/cgs.au, x[-1]/cgs.au)\n",
     "ax.set_ylim(y[0]/cgs.au, y[-1]/cgs.au)\n",
     "\n",

docs/src/1_examples/0_creating_sliceFigures/5_SlicePlot Disk.py

@@ -38,8 +38,8 @@ def makeMovie(prefix, loc, outputloc, model, firstframe,lastframe):
     smooth_rot = sk.smoothMesh(X_rot, Y_rot, Z_rot, dumpData, ['rho'])
 
     #Filmpjes Mats: inferno; -17 -- -12
-    # mesh = ax.pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot["rho"]+1e-99), cmap=plt.cm.get_cmap('gist_heat'), vmin=-19, vmax = -14)
-    mesh = ax.pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot["rho"]+1e-99), cmap=plt.cm.get_cmap('gist_heat'), vmin=-18, vmax = -11.5)
+    # mesh = ax.pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot["rho"]+1e-99), cmap=plt.colormaps['gist_heat'], vmin=-19, vmax = -14)
+    mesh = ax.pcolormesh(X/cgs.au, Y/cgs.au, np.log10(smooth_rot["rho"]+1e-99), cmap=plt.colormaps['gist_heat'], vmin=-18, vmax = -11.5)
     ax.set_xlim(x[0]/cgs.au, x[-1]/cgs.au)
     ax.set_ylim(y[0]/cgs.au, y[-1]/cgs.au)
     ax.set_xlabel('x [au]')

src/plons/AccrDisk.py

@@ -134,7 +134,7 @@ def plot_vrvtRho(axs, smooth,zoom,r=0,limitsRho=False):
             limits = [-17,-11]
     else:
         limits = limitsRho
-    cm  = plt.cm.get_cmap('gist_heat')
+    cm  = plt.colormaps['gist_heat']
 
     ax1.set_xlabel('x [au]',fontsize = 20)
     ax1.set_ylabel('y [au]',fontsize = 20)
@@ -155,7 +155,7 @@ def plot_vrvtRho(axs, smooth,zoom,r=0,limitsRho=False):
     limits = [-40,40]
     # lim = np.abs(np.min(data))
     # limits = [-lim,lim]
-    cm  = plt.cm.get_cmap('seismic')
+    cm  = plt.colormaps['seismic']
     ax2.set_xlabel('x [au]',fontsize = 20)
     ax2.set_aspect('equal')
     ax2.set_facecolor('k')
@@ -172,7 +172,7 @@ def plot_vrvtRho(axs, smooth,zoom,r=0,limitsRho=False):
     # vt
     data = (smooth['smooth_z']['new_vt'])
     limits = [0,200]
-    cm  = plt.cm.get_cmap('nipy_spectral')
+    cm  = plt.colormaps['nipy_spectral']
 
     ax3.set_xlabel('x [au]',fontsize = 20)
     ax3.set_aspect('equal')
@@ -206,7 +206,7 @@ def plot_vrvt(axs,smooth,zoom,r):
     limits = [-40,40]
     # lim = np.abs(np.min(data))
     # limits = [-lim,lim]
-    cm  = plt.cm.get_cmap('seismic')
+    cm  = plt.colormaps['seismic']
     ax2.set_xlabel('x [au]',fontsize = 20)
     ax2.set_ylabel('y [au]',fontsize = 20)
     ax2.set_aspect('equal')
@@ -224,7 +224,7 @@ def plot_vrvt(axs,smooth,zoom,r):
     # vt
     data = (smooth['smooth_z']['new_vt'])
     limits = [0,200]
-    cm  = plt.cm.get_cmap('nipy_spectral')
+    cm  = plt.colormaps['nipy_spectral']
 
     ax3.set_xlabel('x [au]',fontsize = 20)
     ax3.set_aspect('equal')
@@ -256,7 +256,7 @@ def plot_vrRho(axs,smooth,zoom,r):
     limits = [-40,40]
     # lim = np.abs(np.min(data))
     # limits = [-lim,lim]
-    cm  = plt.cm.get_cmap('seismic')
+    cm  = plt.colormaps['seismic']
     ax2.set_xlabel('x [au]',fontsize = 20)
     ax2.set_ylabel('y [au]',fontsize = 20)
     ax2.set_aspect('equal')
@@ -279,7 +279,7 @@ def plot_vrRho(axs,smooth,zoom,r):
     else:
         # limits = [-17,-11]
         limits = [-16,-11]
-    cm  = plt.cm.get_cmap('gist_heat')
+    cm  = plt.colormaps['gist_heat']
 
     ax3.set_xlabel('x [au]',fontsize = 20)
     ax3.set_aspect('equal')

src/plons/Plotting.py

@@ -15,7 +15,7 @@ def plotSlice(ax: plt.Axes,
               smooth: Dict[str, npt.NDArray[np.single]],
               observable: str,
               logplot: bool = False,
-              cmap: matplotlib.colors.Colormap = plt.cm.get_cmap('inferno'),
+              cmap: matplotlib.colors.Colormap = plt.colormaps['inferno'],
               clim: Tuple[Optional[float], Optional[float]] = (None, None)) -> matplotlib.colorbar.Colorbar:
     """Plot a property given a grid and smoothed data ontop of the grid
 
@@ -26,7 +26,7 @@ def plotSlice(ax: plt.Axes,
         smooth (Dict[str, npt.NDArray[np.single]]): Dictionary pointing at smoothed values in meshgrid which you want to plot
         observable (str): Name of the observable you want to plot, corresponding to the name in the smooth directory
         logplot (bool, optional): plot in log scale?. Defaults to False.
-        cmap (matplotlib.colors.Colormap, optional): Colormap to use. Defaults to cm.get_cmap('inferno').
+        cmap (matplotlib.colors.Colormap, optional): Colormap to use. Defaults to plt.colormaps['inferno'].
         clim (Tuple[Optional[float], Optional[float]], optional): limits for the colorbar. Defaults to (None, None).
 
     Returns:
@@ -90,7 +90,7 @@ def SlicePlot2D(ax: plt.Axes,
                 rotate: bool = False,
                 observable: str = "rho",
                 logplot: bool = True,
-                cmap: matplotlib.colors.Colormap = plt.cm.get_cmap('inferno'),
+                cmap: matplotlib.colors.Colormap = plt.colormaps['inferno'],
                 clim: tuple[float, float] = (-17, -14)) -> matplotlib.colorbar.Colorbar:
     """Plot a property given xlims and ylims
 
@@ -104,7 +104,7 @@ def SlicePlot2D(ax: plt.Axes,
         rotate (bool, optional): should the binary be rotated to lay on the x-axis. Defaults to False.
         observable (str, optional): property to plot. Defaults to "rho".
         logplot (bool, optional): plot in log scale?. Defaults to True.
-        cmap (matplotlib.colors.Colormap, optional): colormap to use. Defaults to plt.cm.get_cmap('inferno').
+        cmap (matplotlib.colors.Colormap, optional): colormap to use. Defaults to plt.colormaps['inferno'].
         clim (tuple[float, float], optional): limits of the colormap. Defaults to (-17, -14).
 
     Returns:

src/plons/SlicePlots2D.py

@@ -22,15 +22,15 @@
 
 
 # colormap per parameter
-cm =   {'rho':   plt.cm.get_cmap('inferno'),
-        'speed': plt.cm.get_cmap('CMRmap'),
-        #'Tgas': plt.cm.get_cmap('RdYlGn'),
-        'Tgas':  plt.cm.get_cmap('hot'), #nipy_spectral
-        'tau':   plt.cm.get_cmap('viridis_r'),
-        'tauL':  plt.cm.get_cmap('viridis'),
-        'kappa': plt.cm.get_cmap('Spectral_r'),
-        'Tdust': plt.cm.get_cmap('Spectral_r'),
-        'Gamma': plt.cm.get_cmap('Spectral_r')
+cm =   {'rho':   plt.colormaps['inferno'],
+        'speed': plt.colormaps['CMRmap'],
+        #'Tgas': plt.colormaps['RdYlGn'],
+        'Tgas':  plt.colormaps['hot'], #nipy_spectral
+        'tau':   plt.colormaps['viridis_r'],
+        'tauL':  plt.colormaps['viridis'],
+        'kappa': plt.colormaps['Spectral_r'],
+        'Tdust': plt.colormaps['Spectral_r'],
+        'Gamma': plt.colormaps['Spectral_r']
         }
 
 # label name per parameter
@@ -105,7 +105,7 @@ def smoothData(dumpData, setup, observables, theta = 0., zoom = 1, nneighb = 10,
     - setup         setup data
     - rAccComp      accretion radius of the companion
 '''
-def densityPlot(smooth, zoom, limits, dumpData, setup, orbital=True, cmap=plt.cm.get_cmap('inferno')):
+def densityPlot(smooth, zoom, limits, dumpData, setup, orbital=True, cmap=plt.colormaps['inferno']):
 
     fig, ax = plt.subplots(1, figsize=(7, 7))