Commit 42c120a4 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

matplotlib fixes - make it run on mpl 3.0

parent 881da7b2

README.rst→README.md

+6 −7
Original line number Diff line number Diff line 


pysen

------

-------



PySEN is a Python package that aids experiment planning, data collection, reduction, and analysis 

at the Neutron Spin Echo instrument (SNS-NSE) located at Beam Line 15
@@ -11,23 +11,22 @@ to aid instrument staff in planning, executing, and evaluating experiments perfo 
Oak Ridge National Laboratory, but hopefully will be useful for all NSE users. 

The source code is available at the ORNL git repository https://code.ornl.gov/zp1/pysen. 



Installation

-------------

## Installation

PySEN requires Python 3.7 or newer. Table below shows Python packages that are required to run PySEN.

One of the simplest methods to install Python is to download Anaconda Python (anaconda.com).







|Package     | Minimal version |

|------------|-----------------|

|numpy	     |   1.16          |

|scipy	     |   1.2           |

|matplotlib  |   3.0           |	

|PyQt	     |   5.0           |

|h5py        |   2.9           |

|pandas	     |   0.24          |

|PyQt	     |   5.9           |

|pip	     |  19.0           | 







### Steps



1. Download PySEN from https://code.ornl.gov/zp1/pysen

pysen/plot/__init__.py

+1 −1
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"""

plotting subpackage

"""

from .plotutil    import get_nsubplots                               # NOQA

from .plotutil    import get_nsubplots, get_colormap                 # NOQA

from .qplot       import ( plot_coverage, plot_curscan,              # NOQA

                           plot_diffrun , plot_transmission,         # NOQA

                           plot_datreat)                             # NOQA

pysen/plot/nseplot.py

+14 −18
Original line number Diff line number Diff line
@@ -12,7 +12,6 @@ import logging 
import h5py



import numpy as np

import matplotlib as mpl

import matplotlib.pyplot as plt



from pysen        import version, setup_logger, DEFAULT_LOG_LEVEL
@@ -22,7 +21,8 @@ from pysen.echo import get_symmetry_phase, make_phase_table 
from pysen.plot   import ( plot_echo, plot_atari, plot_map,

                           plot_xyz, plot_magnetic_fields,

                           plot_coverage,

                           plot_diffrun, plot_transmission, plot_datreat)

                           plot_diffrun, plot_transmission, plot_datreat,

                           get_colormap)



def action_default(filenames, **kwargs):

    "default action for echo, atari, etc"
@@ -143,7 +143,6 @@ data = [ 
    if max_limits:

        print('this is not yet implemented')

        return

    else:

    try:

        lcls = locals()

        lcls['np'] = np
@@ -158,10 +157,7 @@ data = [ 
    if not data:

        data = [ coverage(lmax, qmin, pos=pos, mode=mode, tbins=tbins, taus=taus) ]



    try:

        cmap = mpl.colormaps.get_cmap(cmap) 

    except AttributeError:

        pass

    cmap = get_colormap(cmap)

    _ , axes = plt.subplots(figsize=(8,6))

    _ , qlim = plot_coverage(axes, *data, center=center, errors=errors,

                             cmap=cmap, full=full)

pysen/plot/nseplotlib.py

+2 −1
Original line number Diff line number Diff line
@@ -106,7 +106,8 @@ def plot_magnetic_fields(hdfile, iecho=None, **kwargs): 
        fig.suptitle(r'%s | %s | $\lambda$=%.2g$\AA$ $Q$=%.3f$\AA^{-1}$ $\tau$=%.3fns' %

                     (sample, base, lam0/ANGSTROM, q0, tau0))

        log = logging.getLogger()

        for iplt, bsensor in enumerate(reversed(bfield)):

        bfield_list = list(bfield)

        for iplt, bsensor in enumerate(reversed(bfield_list)):

            bmag  = bfield[bsensor]

            label = bsensor.split('.')[-1]

            ax    = axes[iplt//nxplot,iplt%nxplot]

pysen/plot/plotutil.py

+27 −8
Original line number Diff line number Diff line
@@ -4,14 +4,33 @@ plot utilities 
import math

import numpy as np



# def get_color(color):

#     "Get consistent colors for plotting"

#     import colorsys

#     while True:

#         for hue in range(color):

#             hue = 1. * hue / float(color)

#             col = [int(x) for x in colorsys.hsv_to_rgb(hue, 0.667, 230)]

#             yield "#{0:02x}{1:02x}{2:02x}".format(*col)

import matplotlib as mpl

from matplotlib import cm



try:

    _colormaps = mpl.colormaps

    def get_colormap(cmap='hsv'):

        "get color map (new matplotlib 3.7+)"

        return _colormaps.get_cmap(cmap)

except AttributeError:

    def get_colormap(cmap=None):

        "get color map (old matplotlib)"

        cmap = cmap or 'hsv'

        # this is a hack

        return cm.__dict__[cmap]



DEFAULT_CMAP = get_colormap()



CURSCAN_CMAP = { 0: None,

                 1: 'k',

                 2: 'r',

                 3: 'g',

                 4: 'b',

                 5: 'c',

                 6: 'm' }



ALPHA_TRANSPARENT=0.1  # for coverage

ALPHA_OPAQUE=0.9





def get_nsubplots(nplots):