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WIP HBP-75 Merged plotting from tvb-scripts #100

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62 changes: 30 additions & 32 deletions scientific_library/tvb/simulator/plot/base_plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,29 +34,29 @@
"""

import os
import numpy
from tvb.basic.logger.builder import get_logger
from tvb.simulator.plot.config import CONFIGURED

import matplotlib
matplotlib.use(CONFIGURED.MATPLOTLIB_BACKEND)

import numpy
from matplotlib import pyplot
pyplot.rcParams["font.size"] = CONFIGURED.FONTSIZE

from mpl_toolkits.axes_grid1 import make_axes_locatable
from tvb.simulator.plot.utils import ensure_list, generate_region_labels
from tvb.basic.logger.builder import get_logger
from tvb.simulator.plot.config import FiguresConfig, Config
from tvb.simulator.plot.utils import generate_region_labels, ensure_list

matplotlib.use(FiguresConfig().MATPLOTLIB_BACKEND)

pyplot.rcParams["font.size"] = FiguresConfig.FONTSIZE


class BasePlotter(object):

def __init__(self, config=CONFIGURED):
self.config = config
def __init__(self, config=None):
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@liadomide liadomide Apr 10, 2020

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The previous code allowed more unity in the configurations. Currently, the fresh Config() in case of missing init param is always "fresh"

self.config = config or Config()
self.logger = get_logger(self.__class__.__name__)
self.print_regions_indices = True

def _check_show(self):
if self.config.SHOW_FLAG:
if self.config.figures.SHOW_FLAG:
# mp.use('TkAgg')
pyplot.ion()
pyplot.show()
Expand All @@ -66,25 +66,23 @@ def _check_show(self):
pyplot.close()

@staticmethod
def _figure_filename(fig=None, figure_name=None):
if fig is None:
fig = pyplot.gcf()
def _figure_filename(fig=pyplot.gcf(), figure_name=None):
if figure_name is None:
figure_name = fig.get_label()
figure_name = figure_name.replace(": ", "_").replace(" ", "_").replace("\t", "_").replace(",", "")
return figure_name

def _save_figure(self, fig, figure_name=None):
if self.config.SAVE_FLAG:
def _save_figure(self, fig=pyplot.gcf(), figure_name=None):
if self.config.figures.SAVE_FLAG:
figure_name = self._figure_filename(fig, figure_name)
figure_name = figure_name[:numpy.min([100, len(figure_name)])] + '.' + self.config.FIG_FORMAT
figure_dir = self.config.FOLDER_FIGURES
figure_name = figure_name[:numpy.min([100, len(figure_name)])] + '.' + self.config.figures.FIG_FORMAT
figure_dir = self.config.out.FOLDER_FIGURES
if not (os.path.isdir(figure_dir)):
os.mkdir(figure_dir)
pyplot.savefig(os.path.join(figure_dir, figure_name))

@staticmethod
def rect_subplot_shape(self, n, mode="col"):
def rect_subplot_shape(n, mode="col"):
nj = int(numpy.ceil(numpy.sqrt(n)))
ni = int(numpy.ceil(1.0 * n / nj))
if mode.find("row") >= 0:
Expand All @@ -96,7 +94,7 @@ def plot_vector(self, vector, labels, subplot, title, show_y_labels=True, indice
ax = pyplot.subplot(subplot, sharey=sharey)
pyplot.title(title)
n_vector = labels.shape[0]
y_ticks = numpy.array(list(range(n_vector)), dtype=numpy.int32)
y_ticks = numpy.array(range(n_vector), dtype=numpy.int32)
color = 'k'
colors = numpy.repeat([color], n_vector)
coldif = False
Expand Down Expand Up @@ -130,7 +128,7 @@ def plot_vector_violin(self, dataset, vector=[], lines=[], labels=[], subplot=11
ax = pyplot.subplot(subplot, sharey=sharey)
pyplot.title(title)
n_violins = dataset.shape[1]
y_ticks = numpy.array(list(range(n_violins)), dtype=numpy.int32)
y_ticks = numpy.array(range(n_violins), dtype=numpy.int32)
# the vector plot
coldif = False
if indices_red is None:
Expand Down Expand Up @@ -201,7 +199,7 @@ def _plot_matrix(self, matrix, xlabels, ylabels, subplot=111, title="", show_x_l
nticks = []
for ii, (n, tick) in enumerate(zip([nx, ny], ticks)):
if len(tick) == 0:
ticks[ii] = numpy.array(list(range(n)), dtype=numpy.int32)
ticks[ii] = numpy.array(range(n), dtype=numpy.int32)
nticks.append(len(ticks[ii]))
cmap = pyplot.set_cmap(cmap)
img = pyplot.imshow(matrix[ticks[0]][:, ticks[1]].T, cmap=cmap, vmin=vmin, vmax=vmax, interpolation='none')
Expand All @@ -213,10 +211,10 @@ def _plot_matrix(self, matrix, xlabels, ylabels, subplot=111, title="", show_x_l
labels[ii] = generate_region_labels(len(tick), numpy.array(lbls)[tick], ". ",
self.print_regions_indices, tick)
# labels[ii] = numpy.array(["%d. %s" % l for l in zip(tick, lbls[tick])])
getattr(pyplot, xy + "ticks")(numpy.array(list(range(ntick))), labels[ii], rotation=rot)
getattr(pyplot, xy + "ticks")(numpy.array(range(ntick)), labels[ii], rotation=rot)
else:
labels[ii] = numpy.array(["%d." % l for l in tick])
getattr(pyplot, xy + "ticks")(numpy.array(list(range(ntick))), labels[ii])
getattr(pyplot, xy + "ticks")(numpy.array(range(ntick)), labels[ii])
if ind_red is not None:
tck = tick.tolist()
ticklabels = getattr(ax, xy + "axis").get_ticklabels()
Expand All @@ -239,7 +237,7 @@ def plot_regions2regions(self, adj, labels, subplot, title, show_x_labels=True,
x_ticks, y_ticks, indices_red_x, indices_red_y, sharex, sharey, cmap, vmin, vmax)

def _set_axis_labels(self, fig, sub, n_regions, region_labels, indices2emphasize, color='k', position='left'):
y_ticks = list(range(n_regions))
y_ticks = range(n_regions)
# region_labels = numpy.array(["%d. %s" % l for l in zip(y_ticks, region_labels)])
region_labels = generate_region_labels(len(y_ticks), region_labels, ". ", self.print_regions_indices, y_ticks)
big_ax = fig.add_subplot(sub, frameon=False)
Expand All @@ -262,7 +260,7 @@ def plot_in_columns(self, data_dict_list, labels, width_ratios=[], left_ax_focus
right_ax_focus_indices=[], description="", title="", figure_name=None,
figsize=None, **kwargs):
if not isinstance(figsize, (tuple, list)):
figsize = self.config.VERY_LARGE_SIZE
figsize = self.config.figures.VERY_LARGE_SIZE
fig = pyplot.figure(title, frameon=False, figsize=figsize)
fig.suptitle(description)
n_subplots = len(data_dict_list)
Expand Down Expand Up @@ -311,7 +309,7 @@ def plot_in_columns(self, data_dict_list, labels, width_ratios=[], left_ax_focus
def plots(self, data_dict, shape=None, transpose=False, skip=0, xlabels={}, xscales={}, yscales={}, title='Plots',
lgnd={}, figure_name=None, figsize=None):
if not isinstance(figsize, (tuple, list)):
figsize = self.config.VERY_LARGE_SIZE
figsize = self.config.figures.VERY_LARGE_SIZE
if shape is None:
shape = (1, len(data_dict))
fig, axes = pyplot.subplots(shape[0], shape[1], figsize=figsize)
Expand Down Expand Up @@ -343,7 +341,7 @@ def confirm_y_coordinate(data, ymax):
return tuple(data)

if not isinstance(figsize, (tuple, list)):
figsize = self.config.VERY_LARGE_SIZE
figsize = self.config.figures.VERY_LARGE_SIZE

if subtitles is None:
subtitles = keys
Expand Down Expand Up @@ -433,7 +431,7 @@ def barlabel(ax, rects, positions):

if fig is None:
if not isinstance(figsize, (tuple, list)):
figsize = self.config.VERY_LARGE_SIZE
figsize = self.config.figures.VERY_LARGE_SIZE
fig, ax = pyplot.subplots(1, 1, figsize=figsize)
show_and_save = True
else:
Expand All @@ -442,8 +440,8 @@ def barlabel(ax, rects, positions):
ax = pyplot.gca()
if isinstance(data, (list, tuple)): # If, there are many groups, data is a list:
# Fill in with nan in case that not all groups have the same number of elements
from itertools import zip_longest
data = numpy.array(list(zip_longest(*ensure_list(data), fillvalue=numpy.nan))).T
from itertools import izip_longest
data = numpy.array(list(izip_longest(*ensure_list(data), fillvalue=numpy.nan))).T
elif data.ndim == 1: # This is the case where there is only one group...
data = numpy.expand_dims(data, axis=1).T
n_groups, n_elements = data.shape
Expand Down Expand Up @@ -479,7 +477,7 @@ def barlabel(ax, rects, positions):
self._check_show()
return fig, ax

def plot(self, plot_fun_name, *args, **kwargs):
def tvb_plot(self, plot_fun_name, *args, **kwargs):
import tvb.simulator.plot.tools as TVB_plot_tools
getattr(TVB_plot_tools, plot_fun_name)(*args, **kwargs)
fig = pyplot.gcf()
Expand Down
134 changes: 104 additions & 30 deletions scientific_library/tvb/simulator/plot/config.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,47 +34,63 @@
"""

import os
import numpy as np
from datetime import datetime

import numpy


class GenericConfig(object):
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Should not be here!!!!

_module_path = os.path.dirname(__file__)

# Identify and choose the Simulator, or data folder type to read.
MODE_H5 = "H5"
MODE_TVB = "TVB"


class InputConfig(object):
_base_input = os.getcwd()

@property
def HEAD(self):
if self._head_folder is not None:
return self._head_folder

# or else, try to find tvb_data module
try:
import tvb_data
return os.path.dirname(tvb_data.__file__)
except ImportError:
return self._base_input

@property
def IS_TVB_MODE(self):
"""Identify and choose the Input data type to use"""
return self._data_mode == GenericConfig.MODE_TVB

@property
def RAW_DATA_FOLDER(self):
if self._raw_data is not None:
return self._raw_data

return os.path.join(self._base_input, "data", "raw")

def __init__(self, head_folder=None, raw_folder=None, data_mode=GenericConfig.MODE_TVB):
self._head_folder = head_folder
self._raw_data = raw_folder
self._data_mode = data_mode

class FiguresConfig(object):
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We should have here under tvb.simulator.PLOT just a configuration for Figures. This is the single purpose for this module

VERY_LARGE_SIZE = (40, 20)
VERY_LARGE_PORTRAIT = (30, 50)
SUPER_LARGE_SIZE = (80, 40)
LARGE_SIZE = (20, 15)
SMALL_SIZE = (15, 10)
NOTEBOOK_SIZE = (10, 7)
FIG_FORMAT = 'png'
SAVE_FLAG = True
SHOW_FLAG = False
MOUSE_HOOVER = False
MATPLOTLIB_BACKEND = "Agg" # "Qt4Agg"
FONTSIZE = 10
WEIGHTS_NORM_PERCENT = 99
MAX_SINGLE_VALUE = np.finfo("single").max
MAX_INT_VALUE = np.iinfo(np.int64).max

class OutputConfig(object):
subfolder = None

def __init__(self, out_base=None, separate_by_run=False):
print(out_base)
print(separate_by_run)
"""
:param work_folder: Base folder where logs/figures/results should be kept
:param separate_by_run: Set TRUE, when you want logs/results/figures to be in different files / each run
"""
self._out_base = out_base or os.path.join(os.getcwd(), "outputs")
self._separate_by_run = separate_by_run

def largest_size(self):
import sys
if 'IPython' not in sys.modules:
return self.LARGE_SIZE
from IPython import get_ipython
if getattr(get_ipython(), 'kernel', None) is not None:
return self.NOTEBOOK_SIZE
else:
return self.LARGE_SIZE

@property
def FOLDER_LOGS(self):
folder = os.path.join(self._out_base, "logs")
Expand All @@ -91,6 +107,8 @@ def FOLDER_RES(self):
folder = folder + datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M')
if not (os.path.isdir(folder)):
os.makedirs(folder)
if self.subfolder is not None:
folder = os.path.join(folder, self.subfolder)
return folder

@property
Expand All @@ -100,7 +118,63 @@ def FOLDER_FIGURES(self):
folder = folder + datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M')
if not (os.path.isdir(folder)):
os.makedirs(folder)
if self.subfolder is not None:
os.path.join(folder, self.subfolder)
return folder

@property
def FOLDER_TEMP(self):
return os.path.join(self._out_base, "temp")


class FiguresConfig(object):
VERY_LARGE_SIZE = (40, 20)
VERY_LARGE_PORTRAIT = (30, 50)
SUPER_LARGE_SIZE = (80, 40)
LARGE_SIZE = (20, 15)
SMALL_SIZE = (15, 10)
NOTEBOOK_SIZE = (20, 10)
FIG_FORMAT = 'png'
SAVE_FLAG = True
SHOW_FLAG = False
MOUSE_HOOVER = False
MATPLOTLIB_BACKEND = "Agg" # "Qt4Agg"
FONTSIZE = 10
SMALL_FONTSIZE = 8
LARGE_FONTSIZE = 12

def largest_size(self):
import sys
if 'IPython' not in sys.modules:
return self.LARGE_SIZE
from IPython import get_ipython
if getattr(get_ipython(), 'kernel', None) is not None:
return self.NOTEBOOK_SIZE
else:
return self.LARGE_SIZE


class CalculusConfig(object):
# Normalization configuration
WEIGHTS_NORM_PERCENT = 99

# If True a plot will be generated to choose the number of eigenvalues to keep
INTERACTIVE_ELBOW_POINT = False

MIN_SINGLE_VALUE = numpy.finfo("single").min
MAX_SINGLE_VALUE = numpy.finfo("single").max
MAX_INT_VALUE = numpy.iinfo(numpy.int64).max
MIN_INT_VALUE = numpy.iinfo(numpy.int64).max


class Config(object):
generic = GenericConfig()
figures = FiguresConfig()
calcul = CalculusConfig()

def __init__(self, head_folder=None, raw_data_folder=None, output_base=None, separate_by_run=False):
self.input = InputConfig(head_folder, raw_data_folder)
self.out = OutputConfig(output_base, separate_by_run)


CONFIGURED = FiguresConfig()
CONFIGURED = Config()
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