geone 1.3.0__py313-none-manylinux_2_35_x86_64.whl

geone/customcolors.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# -------------------------------------------------------------------------
+# Python module:  'customcolors.py'
+# author:         Julien Straubhaar
+# date:           jan-2018
+# -------------------------------------------------------------------------
+
+"""
+Module for definition of custom colors and colormaps.
+
+**Defined objects in this module**
+
+- "default" color for "bad" value (nan)
+    - `cbad_def = (.9, .9, .9, 0.5)` : default color for "bad" value (nan)
+
+- "default" color map
+    - `cmap_def`
+
+- some colors from "libreoffice" (merci Christoph!)
+    - `col_chart01 = [x/255. for x in (  0,  69, 134)]` : dark blue
+    - `col_chart02 = [x/255. for x in (255,  66,  14)]` : orange
+    - `col_chart03 = [x/255. for x in (255, 211,  32)]` : yellow
+    - `col_chart04 = [x/255. for x in ( 87, 157,  28)]` : green
+    - `col_chart05 = [x/255. for x in (126,   0,  33)]` : dark red
+    - `col_chart06 = [x/255. for x in (131, 202, 255)]` : light blue
+    - `col_chart07 = [x/255. for x in ( 49,  64,   4)]` : dark green
+    - `col_chart08 = [x/255. for x in (174, 207,   0)]` : light green
+    - `col_chart09 = [x/255. for x in ( 75,  31, 111)]` : purple
+    - `col_chart10 = [x/255. for x in (255, 149,  14)]` : dark yellow
+    - `col_chart11 = [x/255. for x in (197,   0,  11)]` : red
+    - `col_chart12 = [x/255. for x in (  0, 132, 209)]` : blue
+
+- ... with other names
+    - `col_chart_purple     = col_chart09`
+    - `col_chart_darkblue   = col_chart01`
+    - `col_chart_blue       = col_chart12`
+    - `col_chart_lightblue  = col_chart06`
+    - `col_chart_green      = col_chart04`
+    - `col_chart_darkgreen  = col_chart07`
+    - `col_chart_lightgreen = col_chart08`
+    - `col_chart_yellow     = col_chart03`
+    - `col_chart_darkyellow = col_chart10`
+    - `col_chart_orange     = col_chart02`
+    - `col_chart_red        = col_chart11`
+    - `col_chart_darkred    = col_chart05`
+
+- ... in list
+    - `col_chart_list = [col_chart01, col_chart02, col_chart03, col_chart04, \
+                        col_chart05, col_chart06, col_chart07, col_chart08, \
+                        col_chart09, col_chart10, col_chart11, col_chart12]`
+    - `col_chart_list_s = [col_chart_list[i] for i in (8, 0, 11, 5, 3, 6, 7, 2, 9, 1, 10, 4)]`
+
+- pre-defined colormaps
+    - `cmap1`, `cmap2`, `cmapW2B` (white to black), `cmapB2W` (black to white)
+"""
+
+import numpy as np
+import matplotlib.colors as mcolors
+import matplotlib.pyplot as plt
+
+from mpl_toolkits import axes_grid1
+
+# ============================================================================
+class CustomcolorsError(Exception):
+    """
+    Custom exception related to `customcolors` module.
+    """
+    pass
+# ============================================================================
+
+# ----------------------------------------------------------------------------
+def add_colorbar(im, aspect=20.0, pad_fraction=1.0, **kwargs):
+    """
+    Adds a vertical color bar to an image plot.
+
+    Parameters
+    ----------
+    im : matplotlib.image.AxesImage
+        image (returned by `matplotlib.pyplot.imshow`)
+
+    aspect : float, default: 20.0
+        aspect ratio height over width of the color bar
+
+    pad_fraction : float, default: 1.0
+        padding fraction with respect to the color bar width; if w is the width
+        of the color bar, then the space between the image and the color bar will
+        be of with `pad_fraction` * w
+
+    kwargs : dict
+        keyword arguments passed to `im.axes.figure.colorbar`
+
+    Notes
+    -----
+    Code from https://nbviewer.jupyter.org/github/mgeier/python-audio/blob/master/plotting/matplotlib-colorbar.ipynb
+    """
+    # fname = 'add_colorbar'
+
+    divider = axes_grid1.make_axes_locatable(im.axes)
+    width = axes_grid1.axes_size.AxesY(im.axes, aspect=1./aspect)
+    pad = axes_grid1.axes_size.Fraction(pad_fraction, width)
+    current_ax = plt.gca()
+    cax = divider.append_axes("right", size=width, pad=pad)
+    plt.sca(current_ax)
+    return im.axes.figure.colorbar(im, cax=cax, **kwargs)
+# ----------------------------------------------------------------------------
+
+# ----------------------------------------------------------------------------
+def custom_cmap(
+        cseq,
+        vseq=None,
+        ncol=256,
+        cunder=None,
+        cover=None,
+        cbad=None,
+        alpha=None,
+        cmap_name='custom_cmap',
+        logger=None):
+    """
+    Defines a custom color map given colors at transition values.
+
+    Parameters
+    ----------
+    cseq : 1D array-like
+        sequence of colors, each color is given by a
+        3-tuple (RGB code), 4-tuple (RGBA code) or string
+
+    vseq : 1D array-like of floats, optional
+        sequence of increasing values of same length as `cseq`, values that
+        correspond to the colors given in `cseq` in the output color map;
+        by default (`None`): equally spaced values (from 0 to 1) are used
+
+    ncol : int, default: 256
+        number of colors for the color map
+
+    cunder : object defining a color (e.g. 3-tuple, str), optional
+        color (3-tuple (RGB code), 4-tuple (RGBA code) or str), used for
+        "under" values
+
+    cover : object defining a color (e.g. 3-tuple, str), optional
+        color (3-tuple (RGB code), 4-tuple (RGBA code) or str), used for
+        "over" values
+
+    cbad : object defining a color (e.g. 3-tuple, str), optional
+        color (3-tuple (RGB code), 4-tuple (RGBA code) or str), used for
+        "bad" values
+
+    alpha : 1D array-like of floats, or float, optional
+        values of the "alpha" channel (for transparency), for each color in
+        `cseq` (if a `alpha` is a float, the same value is used for every color)
+
+    cmap_name : str, default: 'custom_cmap'
+        name of the output color map
+
+    logger : :class:`logging.Logger`, optional
+        logger (see package `logging`)
+        if specified, messages are written via `logger` (no print)
+
+    Returns
+    -------
+    colormap : `matplotlib.colors.LinearSegmentedColormap`
+        color map
+
+    Examples
+    --------
+        >>> # # Import if needed
+        >>> # import numpy as np
+        >>> # import matplotlib.pyplot as plt
+        >>> #
+        >>> # Set min and max value to be displayed
+        >>> vmin, vmax = -1.0, 3.0
+        >>> #
+        >>> # Create a custom colormap
+        >>> #   - from blue to white for values from vmin to 0
+        >>> #   - from white to red for values from 0 to vmax
+        >>> #   - with specified colors for "under", "over" and "bad" values
+        >>> my_cmap = custom_cmap(
+        >>>     ('blue', 'white', 'red'), vseq=(vmin,0,vmax),
+        >>>     cunder='cyan', cover='violet', cbad='gray', alpha=1)
+        >>> #
+        >>> # Array of values to display
+        >>> zz = np.linspace(-2, 4, 500).reshape(10, 50)
+        >>> zz[:, 20:25] = np.nan
+        >>> #
+        >>> # Show the array, specifiying min, max and the color map
+        >>> im = plt.imshow(zz, vmin=vmin, vmax=vmax, cmap=my_cmap)
+        >>> add_colorbar(im, aspect=5., extend='both') # add color bar
+        >>> plt.show()
+    """
+    fname = 'custom_cmap'
+
+    # Set alpha sequence
+    if alpha is None:
+        alpha = 1.0
+    aseq = np.asarray(alpha, dtype=float) # numpy.ndarray (possibly 0-dimensional)
+    if aseq.size == 1:
+        aseq = aseq.flat[0] * np.ones(len(cseq))
+    elif aseq.size != len(cseq):
+        err_msg = f'{fname}: length of `alpha` not compatible with `cseq`'
+        if logger: logger.error(err_msg)
+        raise CustomcolorsError(err_msg)
+
+    # Set vseqn: sequence of values rescaled in [0,1]
+    if vseq is not None:
+        if len(vseq) != len(cseq):
+            err_msg = f'{fname}: length of `vseq` and length of `cseq` differ'
+            if logger: logger.error(err_msg)
+            raise CustomcolorsError(err_msg)
+
+        if sum(np.diff(vseq) <= 0.0 ):
+            err_msg = f'{fname}: `vseq` is not an increasing sequence'
+            if logger: logger.error(err_msg)
+            raise CustomcolorsError(err_msg)
+
+        # Linearly rescale vseq on [0,1]
+        vseqn = (np.array(vseq,dtype=float) - vseq[0]) / (vseq[-1] - vseq[0])
+
+    else:
+        vseqn = np.linspace(0,1,len(cseq))
+
+    # Set cseqRGB: sequence of colors as RGB-tuples
+    cseqRGB = []
+    for c in cseq:
+        try:
+            cseqRGB.append(mcolors.ColorConverter().to_rgb(c))
+        except:
+            cseqRGB.append(c)
+
+    # Set dictionary to define the color map
+    cdict = {
+        'red'  :[(vseqn[i], cseqRGB[i][0], cseqRGB[i][0]) for i in range(len(cseq))],
+        'green':[(vseqn[i], cseqRGB[i][1], cseqRGB[i][1]) for i in range(len(cseq))],
+        'blue' :[(vseqn[i], cseqRGB[i][2], cseqRGB[i][2]) for i in range(len(cseq))],
+        'alpha':[(vseqn[i], aseq[i],       aseq[i])       for i in range(len(cseq))]
+        }
+
+    cmap = mcolors.LinearSegmentedColormap(cmap_name, cdict, N=ncol)
+
+    if cunder is not None:
+        try:
+            cmap.set_under(mcolors.ColorConverter().to_rgba(cunder))
+        except:
+            cmap.set_under(cunder)
+
+    if cover is not None:
+        try:
+            cmap.set_over(mcolors.ColorConverter().to_rgba(cover))
+        except:
+            cmap.set_over(cover)
+
+    if cbad is not None:
+        try:
+            cmap.set_bad(mcolors.ColorConverter().to_rgba(cbad))
+        except:
+            cmap.set_bad(cbad)
+
+    return cmap
+# ----------------------------------------------------------------------------
+
+# Default colormap for function in geone
+# ======================================
+cmap_def = 'viridis'
+
+# Some colors and colormaps
+# =========================
+
+# Chart color from libreoffice (merci Christoph)
+col_chart01 = [x/255. for x in (  0,  69, 134)]   # dark blue
+col_chart02 = [x/255. for x in (255,  66,  14)]   # orange
+col_chart03 = [x/255. for x in (255, 211,  32)]   # yellow
+col_chart04 = [x/255. for x in ( 87, 157,  28)]   # green
+col_chart05 = [x/255. for x in (126,   0,  33)]   # dark red
+col_chart06 = [x/255. for x in (131, 202, 255)]   # light blue
+col_chart07 = [x/255. for x in ( 49,  64,   4)]   # dark green
+col_chart08 = [x/255. for x in (174, 207,   0)]   # light green
+col_chart09 = [x/255. for x in ( 75,  31, 111)]   # purple
+col_chart10 = [x/255. for x in (255, 149,  14)]   # dark yellow
+col_chart11 = [x/255. for x in (197,   0,  11)]   # red
+col_chart12 = [x/255. for x in (  0, 132, 209)]   # blue
+
+# ... other names
+col_chart_purple     = col_chart09
+col_chart_darkblue   = col_chart01
+col_chart_blue       = col_chart12
+col_chart_lightblue  = col_chart06
+col_chart_green      = col_chart04
+col_chart_darkgreen  = col_chart07
+col_chart_lightgreen = col_chart08
+col_chart_yellow     = col_chart03
+col_chart_darkyellow = col_chart10
+col_chart_orange     = col_chart02
+col_chart_red        = col_chart11
+col_chart_darkred    = col_chart05
+
+# ... list
+col_chart_list = [col_chart01, col_chart02, col_chart03, col_chart04,
+                  col_chart05, col_chart06, col_chart07, col_chart08,
+                  col_chart09, col_chart10, col_chart11, col_chart12]
+
+# ... list reordered
+col_chart_list_s = [col_chart_list[i] for i in (8, 0, 11, 5, 3, 6, 7, 2, 9, 1, 10, 4)]
+
+# Default color for bad value (nan)
+cbad_def = (.9, .9, .9, 0.5)
+
+# Pre-defined colormaps
+# =====================
+
+# colormap cmap1 / cmap1_alpha (increasing alpha values)
+# --------------
+cbad1   = (.9, .9, .9, 0.5)
+# cunder1 = [x/255. for x in (160, 40, 160)] + [0.5] # +[0.5] ... for appending alpha channel
+# cover1  = [x/255. for x in (250,  80, 120)] + [0.5] # +[0.5] ... for appending alpha channel
+cunder1 = [x/255. for x in (200, 10, 250)] + [0.5] # +[0.5] ... for appending alpha channel
+cover1  = [x/255. for x in (250,  10, 10)] + [0.5] # +[0.5] ... for appending alpha channel
+cmaplist1 = ([x/255. for x in (160,  40, 240)],
+             [x/255. for x in (  0, 240, 240)],
+             [x/255. for x in (240, 240,   0)],
+             [x/255. for x in (180,  10,  10)])
+cmap1 = custom_cmap(cmaplist1, cunder=cunder1, cover=cover1, cbad=cbad1, alpha=1.0)
+cmap1_alpha = custom_cmap(cmaplist1, alpha=np.linspace(0, 1, len(cmaplist1)), cunder=cunder1, cover=cover1, cbad=cbad1)
+
+# colormap cmap2 / cmap2_alpha (increasing alpha values)
+# --------------
+cmaplist2 = ['purple', 'blue', 'cyan', 'yellow', 'red', 'black']
+cbad2   = cbad_def
+cunder2 = cbad_def
+cover2  = cbad_def
+cmap2 = custom_cmap(cmaplist2, cunder=cunder2, cover=cover2, cbad=cbad2, alpha=1.0)
+cmap2_alpha = custom_cmap(cmaplist2, alpha=np.linspace(0, 2, len(cmaplist2)), cunder=cunder2, cover=cover2, cbad=cbad2)
+
+# colormap cmapW2B / cmapB2W (white to black / black to white)
+# --------------
+cmapW2B = custom_cmap(['white', 'black'], cunder=(0.0, 0.0, 1.0, 0.5), cover=(1.0, 0.0, 0.0, 0.5), cbad=col_chart_yellow+[0.5], alpha=1.0)
+cmapB2W = custom_cmap(['black', 'white'], cunder=(0.0, 0.0, 1.0, 0.5), cover=(1.0, 0.0, 0.0, 0.5), cbad=col_chart_yellow+[0.5], alpha=1.0)
+
+# "Extended" existing colormap from matplotlib, by adding specific colors for under values, over values and bad values
+# # Example for cmap 'terrain'
+# cmap_terrain_ext = custom_cmap([plt.get_cmap('terrain')(x) for x in np.linspace(0, 1, 256)], ncol=256, cunder='pink', cover='orange', cbad='red')
+# # or:
+# cmap_terrain_ext = plt.get_cmap('terrain')
+# cmap_terrain_ext.set_under('pink')
+# cmap_terrain_ext.set_over('orange')
+# cmap_terrain_ext.set_bad('red')
+# ----------------------------------------------------------------------------
+#
+# # Notes:
+# # =====
+# # To show available colormaps in matplotlib:
+# plt.colormaps()
+#
+# # To show some colormaps (LinearSegmentedColormap) from matplotlib:
+# cm_name = [name for name in plt.cm.datad.keys()]
+# cmap = plt.get_cmap('ocean')  # get the colormap named 'ocean' (cm_name[105])
+#
+# # To get current rcParams (matplotlib)
+# import matplotlib
+# matplotlib.rcParams
+#
+# # Useful function to convert color from/to rgb[a]/hex:
+# import matplotlib
+# matplotlib.mcolors.to_rgb()
+# matplotlib.mcolors.to_rgba()
+# matplotlib.mcolors.to_hex()
+# matplotlib.mcolors.to_hex(,keep_alpha=True)
+# ----------------------------------------------------------------------------
+
+if __name__ == "__main__":
+    print("Module 'geone.customcolors' example:")
+    import matplotlib.pyplot as plt
+
+    # Plot a function of two variable in a given domain
+    # Set domain and number of cell in each direction
+    xmin, xmax = -2, 2
+    ymin, ymax = -1, 2
+    nx, ny = 200, 150
+
+    # Set the cell size
+    sx, sy = (xmax-xmin)/nx, (ymax-ymin)/ny
+
+    # Set the meshgrid
+    x, y = xmin + 0.5 * sx + sx * np.arange(nx), ymin + 0.5 * sy + sy * np.arange(ny)
+    # # equivalently:
+    # x, y = np.arange(xmin+sx/2, xmax, sx), np.arange(ymin+sy/2, ymax ,sy)
+    # x, y = np.linspace(xmin+sx/2, xmax-sx/2, nx), np.linspace(ymin+sy/2, ymax-sy/2, ny)
+    xx,yy = np.meshgrid(x,y)
+
+    # Set the function values
+    zz = xx**2 + yy**2 - 2
+    zz[np.where(zz < -1.7)] = np.nan
+
+    # Specify some points in the grid
+    px = np.arange(xmin,xmax,.1)
+    py = np.zeros(len(px))
+    pz = px**2 + py**2 - 2
+    pz[np.where(pz < -1.7)] = np.nan
+
+    # Set min and max value to be displayed
+    vmin, vmax = -1.0, 3.0
+
+    # Create a custom colormap
+    my_cmap = custom_cmap(('blue', 'white', 'red'), vseq=(vmin,0,vmax),
+                          cunder='cyan', cover='violet', cbad='gray', alpha=.3)
+
+    # Display
+    fig, ax = plt.subplots(2,2,figsize=(16,10))
+    # --- 1st plot ---
+    cax = ax[0,0]
+    im_plot = cax.imshow(zz, cmap=cmap1, vmin=vmin, vmax=vmax, origin='lower',
+                         extent=[xmin, xmax, ymin, ymax], interpolation='none')
+    cax.set_xlim(xmin, xmax)
+    cax.set_ylim(ymin, ymax)
+    cax.grid()
+    cax.set_xlabel("x-axis")
+    cax.set_xticks([-1, 1])
+    cax.set_xticklabels(['x=-1', 'x=1'], fontsize=8)
+
+    # cbarShrink = 0.9
+    # plt.colorbar(extend='both', shrink=cbarShrink, aspect=20*cbarShrink)
+    add_colorbar(im_plot, extend='both')
+
+    # add points
+    col = [0 for i in range(len(pz))]
+    for i in range(len(pz)):
+        if ~ np.isnan(pz[i]):
+            col[i] = cmap1((pz[i]-vmin)/(vmax-vmin))
+        else:
+            col[i] = mcolors.ColorConverter().to_rgba(cbad1)
+
+    cax.scatter(px, py, marker='o', s=50, edgecolor='black', color=col)
+    cax.set_title('colormap: cmap1')
+
+    # --- 2nd plot ---
+    plt.subplot(2,2,2)
+    im_plot = plt.imshow(zz,cmap=my_cmap, vmin=vmin, vmax=vmax, origin='lower',
+                         extent=[xmin, xmax, ymin, ymax], interpolation='none')
+    plt.grid()
+
+    cbar = add_colorbar(im_plot, ticks=[vmin,vmax])
+    # cbar.ax.set_yticklabels(cbar.get_ticks(), fontsize=16)
+    cbar.set_ticks([vmin, 0, vmax])
+    cbar.ax.set_yticklabels([f'min={vmin}', 0, f'max={vmax}'], fontsize=16)
+
+    col = [0 for i in range(len(pz))]
+    for i in range(len(pz)):
+        if not np.isnan(pz[i]):
+            col[i] = my_cmap((pz[i]-vmin)/(vmax-vmin))
+        else:
+            col[i] = mcolors.ColorConverter().to_rgba('gray')
+
+    # add points
+    plt.scatter(px, py, marker='o', s=50, edgecolor='black', color=col)
+
+    plt.title('colormap: my_cmap')
+
+    # --- 3rd plot ---
+    plt.subplot(2,2,3)
+    im_plot = plt.imshow(zz, cmap=custom_cmap(col_chart_list, ncol=len(col_chart_list)),
+                         vmin=vmin, vmax=vmax, origin='lower',
+                         extent=[xmin,xmax,ymin,ymax], interpolation='none')
+    plt.grid()
+    # plt.colorbar(shrink=cbarShrink, aspect=20*cbarShrink)
+    add_colorbar(im_plot)
+
+    #col = custom_cmap(col_chart_list, ncol=len(col_chart_list))((pz-vmin)/(vmax-vmin))
+    col = [0 for i in range(len(pz))]
+    for i in range(len(pz)):
+        if ~ np.isnan(pz[i]):
+            col[i] = custom_cmap(col_chart_list, ncol=len(col_chart_list))((pz[i]-vmin)/(vmax-vmin))
+        else:
+            col[i] = mcolors.ColorConverter().to_rgba('white')
+
+    plt.scatter(px, py, marker='o', s=50, edgecolor='black', color=col)
+
+    plt.title('colormap: col_chart_list')
+
+    # --- 4th plot ---
+    plt.subplot(2,2,4)
+    im_plot = plt.imshow(zz, cmap=custom_cmap(col_chart_list_s,
+                                              ncol=len(col_chart_list_s)),
+                         vmin=vmin, vmax=vmax, origin='lower',
+                         extent=[xmin, xmax, ymin, ymax], interpolation='none')
+    plt.grid()
+    # plt.colorbar(shrink=cbarShrink, aspect=20*cbarShrink)
+    add_colorbar(im_plot)
+
+    #col = custom_cmap(col_chart_list_s, ncol=len(col_chart_list_s))((pz-vmin)/(vmax-vmin))
+    col = [0 for i in range(len(pz))]
+    for i in range(len(pz)):
+        if ~ np.isnan(pz[i]):
+            col[i] = custom_cmap(col_chart_list_s, ncol=len(col_chart_list_s))((pz[i]-vmin)/(vmax-vmin))
+        else:
+            col[i] = mcolors.ColorConverter().to_rgba('white')
+
+    plt.scatter(px, py, marker='o', s=50, edgecolor='black', color=col)
+
+    plt.title('colormap: col_chart_list_s')
+
+    # main title
+    plt.suptitle(r'$z=x^2 + y^2 - 2$', fontsize=24)
+
+    # plt.tight_layout()
+
+    # fig.show()
+    plt.show()
+
+    a = input("Press enter to continue...")

geone/deesse_core/__init__.py

@@ -0,0 +1,5 @@
+# import all modules...
+try:
+    import geone.deesse_core.deesse
+except ImportError:
+    pass