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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2012-2018 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# .
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
# .
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""Semi-graphical tool for peak-picking and extracting visually control points
from an image with Debye-Scherer rings"""
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "08/01/2021"
__status__ = "production"
import os
import sys
import threading
import logging
import gc
import operator
import numpy
import fabio
logger = logging.getLogger(__name__)
try:
from silx.gui import qt
except ImportError:
logger.debug("Backtrace", exc_info=True)
qt = None
if qt is not None:
from .utils import update_fig, maximize_fig
from .matplotlib import matplotlib, pyplot, pylab
from . import utils as gui_utils
from ..control_points import ControlPoints
from ..calibrant import CALIBRANT_FACTORY
from ..blob_detection import BlobDetection
from ..massif import Massif
from ..ext.reconstruct import reconstruct
from ..ext.watershed import InverseWatershed
class PeakPicker(object):
"""
This class is in charge of peak picking, i.e. find bragg spots in the image
Two methods can be used : massif or blob
"""
VALID_METHODS = ["massif", "blob", "watershed"]
help = ["Please select rings on the diffraction image. In parenthesis, some modified shortcuts for single button mouse (Apple):",
" * Right-click (click+n): try an auto find for a ring",
" * Right-click + Ctrl (click+b): create new group with one point",
" * Right-click + Shift (click+v): add one point to current group",
" * Right-click + m (click+m): find more points for current group",
" * Center-click or (click+d): erase current group",
" * Center-click + 1 or (click+1): erase closest point from current group"]
def __init__(self, data, reconst=False, mask=None,
pointfile=None, calibrant=None, wavelength=None, detector=None,
method="massif"):
"""
:param data: input image as numpy array
:param reconst: shall masked part or negative values be reconstructed (wipe out problems with pilatus gaps)
:param mask: area in which keypoints will not be considered as valid
:param pointfile:
"""
if isinstance(data, (str,)):
self.data = fabio.open(data).data.astype("float32")
else:
self.data = numpy.ascontiguousarray(data, numpy.float32)
if mask is not None:
mask = mask.astype(bool)
view = self.data.ravel()
flat_mask = mask.ravel()
min_valid = view[numpy.where(flat_mask == False)].min()
view[numpy.where(flat_mask)] = min_valid
self.shape = self.data.shape
self.points = ControlPoints(pointfile, calibrant=calibrant, wavelength=wavelength)
self.fig = None
self.fig2 = None
self.fig2sp = None
self.ax = None
self.ct = None
self.msp = None
self.append_mode = None
self.spinbox = None
self.refine_btn = None
self.ref_action = None
self.sb_action = None
self.reconstruct = reconst
self.detector = detector
self.mask = mask
self.massif = None # used for massif detection
self.blob = None # used for blob detection
self.watershed = None # used for inverse watershed
self._sem = threading.Semaphore()
self.mpl_connectId = None
self.defaultNbPoints = 100
self._init_thread = None
self.point_filename = None
self.callback = None
self.method = None
if method not in self.VALID_METHODS:
logger.error("Not a valid peak-picker method: %s should be part of %s", method, self.VALID_METHODS)
method = self.VALID_METHODS[0]
self.init(method, False)
def init(self, method, sync=True):
"""
Unified initializer
"""
assert method in self.VALID_METHODS
if method != self.method:
self.__getattribute__("_init_" + method)(sync)
self.method = method
def sync_init(self):
if self._init_thread:
self._init_thread.join()
def _init_massif(self, sync=True):
"""
Initialize PeakPicker for massif based detection
"""
if self.reconstruct:
if self.mask is None:
self.mask = self.data < 0
data = reconstruct(self.data, self.mask)
else:
data = self.data
self.massif = Massif(data)
self._init_thread = threading.Thread(target=self.massif.get_labeled_massif, name="massif_process")
self._init_thread.start()
if sync:
self._init_thread.join()
def _init_blob(self, sync=True):
"""
Initialize PeakPicker for blob based detection
"""
if self.mask is not None:
self.blob = BlobDetection(self.data, mask=self.mask)
else:
self.blob = BlobDetection(self.data, mask=(self.data < 0))
self._init_thread = threading.Thread(target=self.blob.process, name="blob_process")
self._init_thread.start()
if sync:
self._init_thread.join()
def _init_watershed(self, sync=True):
"""
Initialize PeakPicker for watershed based detection
"""
self.watershed = InverseWatershed(self.data)
self._init_thread = threading.Thread(target=self.watershed.init, name="iw_init")
self._init_thread.start()
if sync:
self._init_thread.join()
def peaks_from_area(self, **kwargs):
"""
Return the list of peaks within an area
:param mask: 2d array with mask.
:param Imin: minimum of intensity above the background to keep the point
:param keep: maximum number of points to keep
:param method: enforce the use of detection using "massif" or "blob" or "watershed"
:param ring: ring number to which assign the points
:param dmin: minimum distance between two peaks (in pixels)
:param seed: good starting points.
:return: list of peaks [y,x], [y,x], ...]
"""
method = kwargs.get("method")
ring = kwargs.get("ring", 0)
if not method:
method = self.method
else:
self.init(method, True)
obj = self.__getattribute__(method)
points = obj.peaks_from_area(**kwargs)
if points:
gpt = self.points.append(points, ring)
if self.fig:
npl = numpy.array(points)
gpt.plot = self.ax.plot(npl[:, 1], npl[:, 0], "o", scalex=False, scaley=False)
pt0x = gpt.points[0][1]
pt0y = gpt.points[0][0]
gpt.annotate = self.ax.annotate(gpt.label, xy=(pt0x, pt0y), xytext=(pt0x + 10, pt0y + 10),
weight="bold", size="large", color="black",
arrowprops=dict(facecolor='white', edgecolor='white'))
update_fig(self.fig)
return points
def reset(self):
"""
Reset control point and graph (if needed)
"""
self.points.reset()
if self.fig and self.ax:
# empty annotate and plots
if len(self.ax.texts) > 0:
self.ax.texts = []
if len(self.ax.lines) > 0:
self.ax.lines = []
# Redraw the image
if not gui_utils.main_loop:
self.fig.show()
update_fig(self.fig)
def gui(self, log=False, maximize=False, pick=True):
"""
:param log: show z in log scale
"""
if self.fig is None:
self.fig = pyplot.figure()
self.fig.subplots_adjust(right=0.75)
# add 3 subplots at the same position for debye-sherrer image, contour-plot and massif contour
self.ax = self.fig.add_subplot(111)
self.ct = self.fig.add_subplot(111)
self.msp = self.fig.add_subplot(111)
toolbar = self.fig.canvas.toolbar
toolbar.addSeparator()
a = toolbar.addAction('Opts', self.on_option_clicked)
a.setToolTip('open options window')
if pick:
label = qt.QLabel("Ring #", toolbar)
toolbar.addWidget(label)
self.spinbox = qt.QSpinBox(toolbar)
self.spinbox.setMinimum(0)
self.sb_action = toolbar.addWidget(self.spinbox)
a = toolbar.addAction('Refine', self.on_refine_clicked)
a.setToolTip('switch to refinement mode')
self.ref_action = a
self.mpl_connectId = self.fig.canvas.mpl_connect('button_press_event', self.onclick)
if log:
data_disp = numpy.log1p(self.data - self.data.min())
txt = 'Log colour scale (skipping lowest/highest per mille)'
else:
data_disp = self.data
txt = 'Linear colour scale (skipping lowest/highest per mille)'
# skip lowest and highest per mille of image values via vmin/vmax
sorted_list = data_disp.flatten() # explicit copy
sorted_list.sort()
show_min = sorted_list[int(round(1e-3 * (sorted_list.size - 1)))]
show_max = sorted_list[int(round(0.999 * (sorted_list.size - 1)))]
im = self.ax.imshow(data_disp, vmin=show_min, vmax=show_max,
origin="lower", interpolation="nearest",
)
self.ax.set_ylabel('y in pixels')
self.ax.set_xlabel('x in pixels')
if self.detector:
s1, s2 = self.data.shape
s1 -= 1
s2 -= 1
self.ax.set_xlim(0, s2)
self.ax.set_ylim(0, s1)
d1 = numpy.array([0, s1, s1, 0])
d2 = numpy.array([0, 0, s2, s2])
p1, p2, _ = self.detector.calc_cartesian_positions(d1=d1, d2=d2)
ax = self.fig.add_subplot(1, 1, 1,
xbound=False,
ybound=False,
xlabel=r'dim2 ($\approx m$)',
ylabel=r'dim1 ($\approx m$)',
xlim=(p2.min(), p2.max()),
ylim=(p1.min(), p1.max()),
aspect='equal',
zorder=-1)
ax.xaxis.set_label_position('top')
ax.yaxis.set_label_position('right')
ax.yaxis.label.set_color('blue')
ax.xaxis.label.set_color('blue')
ax.tick_params(colors="blue", labelbottom='off', labeltop='on',
labelleft='off', labelright='on')
# ax.autoscale_view(False, False, False)
else:
_cbar = self.fig.colorbar(im, label=txt)
# self.ax.autoscale_view(False, False, False)
update_fig(self.fig)
if maximize:
maximize_fig(self.fig)
if not gui_utils.main_loop:
self.fig.show()
def load(self, filename):
"""
load a filename and plot data on the screen (if GUI)
"""
self.points.load(filename)
self.display_points()
def display_points(self, minIndex=0, reset=False):
"""
display all points and their ring annotations
:param minIndex: ring index to start with
:param reset: remove all point before re-displaying them
"""
if self.ax is not None:
if reset:
self.ax.texts = []
self.ax.lines = []
for _lbl, gpt in self.points._groups.items():
idx = gpt.ring
if idx < minIndex:
continue
if len(gpt) > 0:
pt0x = gpt.points[0][1]
pt0y = gpt.points[0][0]
gpt.annotate = self.ax.annotate(gpt.label, xy=(pt0x, pt0y), xytext=(pt0x + 10, pt0y + 10),
weight="bold", size="large", color="black",
arrowprops=dict(facecolor='white', edgecolor='white'))
npl = numpy.array(gpt.points)
gpt.plot = self.ax.plot(npl[:, 1], npl[:, 0], "o", scalex=False, scaley=False)
def remove_grp(self, lbl):
"""
remove a group of points
:param lbl: label of the group of points
"""
gpt = self.points.pop(lbl=lbl)
if gpt and self.ax:
print(gpt.annotate)
if gpt.annotate in self.ax.texts:
self.ax.texts.remove(gpt.annotate)
for plot in gpt.plot:
if plot in self.ax.lines:
self.ax.lines.remove(plot)
update_fig(self.fig)
def onclick(self, event):
"""
Called when a mouse is clicked
"""
def annontate(x, x0=None, idx=None, gpt=None):
"""
Call back method to annotate the figure while calculation are going on ...
:param x: coordinates
:param x0: coordinates of the starting point
:param gpt: group of point, instance of PointGroup
TODO
"""
if x0 is None:
annot = self.ax.annotate(".", xy=(x[1], x[0]), weight="bold", size="large", color="black")
else:
if gpt:
annot = self.ax.annotate(gpt.label, xy=(x[1], x[0]), xytext=(x0[1], x0[0]),
weight="bold", size="large", color="black",
arrowprops=dict(facecolor='white', edgecolor='white'),)
gpt.annotate = annot
else:
annot = self.ax.annotate("%i" % (len(self.points)), xy=(x[1], x[0]), xytext=(x0[1], x0[0]),
weight="bold", size="large", color="black",
arrowprops=dict(facecolor='white', edgecolor='white'),)
update_fig(self.fig)
return annot
def common_creation(points, gpt=None):
"""
plot new set of points
:param points: list of points
:param gpt: : group of point, instance of PointGroup
"""
if points:
if not gpt:
gpt = self.points.append(points, ring=self.spinbox.value())
npl = numpy.array(points)
gpt.plot = self.ax.plot(npl[:, 1], npl[:, 0], "o", scalex=False, scaley=False)
update_fig(self.fig)
sys.stdout.flush()
return gpt
def new_grp(event):
" * new_grp Right-click (click+n): try an auto find for a ring"
# ydata is a float, and matplotlib display pixels centered.
# we use floor (int cast) instead of round to avoid use of
# banker's rounding
ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
points = self.massif.find_peaks([ypix, xpix],
self.defaultNbPoints,
None, self.massif_contour)
if points:
gpt = common_creation(points)
annontate(points[0], [ypix, xpix], gpt=gpt)
logger.info("Created group #%2s with %i points", gpt.label, len(gpt))
else:
logger.warning("No peak found !!!")
def single_point(event):
" * Right-click + Ctrl (click+b): create new group with one single point"
ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
newpeak = self.massif.nearest_peak([ypix, xpix])
if newpeak:
gpt = common_creation([newpeak])
annontate(newpeak, [ypix, xpix], gpt=gpt)
logger.info("Create group #%2s with single point x=%5.1f, y=%5.1f", gpt.label, newpeak[1], newpeak[0])
else:
logger.warning("No peak found !!!")
def append_more_points(event):
" * Right-click + m (click+m): find more points for current group"
gpt = self.points.get(self.spinbox.value())
if not gpt:
new_grp(event)
return
if gpt.plot:
if gpt.plot[0] in self.ax.lines:
self.ax.lines.remove(gpt.plot[0])
update_fig(self.fig)
# matplotlib coord to pixel coord, avoinding use of banker's round
ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
# need to annotate only if a new group:
listpeak = self.massif.find_peaks([ypix, xpix],
self.defaultNbPoints, None,
self.massif_contour)
if listpeak:
gpt.points += listpeak
logger.info("Added %i points to group #%2s (now %i points)", len(listpeak), len(gpt.label), len(gpt))
else:
logger.warning("No peak found !!!")
common_creation(gpt.points, gpt)
def append_1_point(event):
" * Right-click + Shift (click+v): add one point to current group"
gpt = self.points.get(self.spinbox.value())
if not gpt:
new_grp(event)
return
if gpt.plot:
if gpt.plot[0] in self.ax.lines:
self.ax.lines.remove(gpt.plot[0])
update_fig(self.fig)
# matplotlib coord to pixel coord, avoinding use of banker's round
ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
newpeak = self.massif.nearest_peak([ypix, xpix])
if newpeak:
gpt.points.append(newpeak)
logger.info("x=%5.1f, y=%5.1f added to group #%2s", newpeak[1], newpeak[0], gpt.label)
else:
logger.warning("No peak found !!!")
common_creation(gpt.points, gpt)
def erase_grp(event):
" * Center-click or (click+d): erase current group"
ring = self.spinbox.value()
gpt = self.points.pop(ring)
if not gpt:
logger.warning("No group of points for ring %s", ring)
return
# print("Remove group from ring %s label %s" % (ring, gpt.label))
if gpt.annotate:
if gpt.annotate in self.ax.texts:
self.ax.texts.remove(gpt.annotate)
if gpt.plot:
if gpt.plot[0] in self.ax.lines:
self.ax.lines.remove(gpt.plot[0])
if len(gpt) > 0:
logger.info("Removing group #%2s containing %i points", gpt.label, len(gpt))
else:
logger.info("No groups to remove")
update_fig(self.fig)
sys.stdout.flush()
def erase_1_point(event):
" * Center-click + 1 or (click+1): erase closest point from current group"
ring = self.spinbox.value()
gpt = self.points.get(ring)
if not gpt:
logger.warning("No group of points for ring %s", ring)
return
# print("Remove 1 point from group from ring %s label %s" % (ring, gpt.label))
if gpt.annotate:
if gpt.annotate in self.ax.texts:
self.ax.texts.remove(gpt.annotate)
if gpt.plot:
if gpt.plot[0] in self.ax.lines:
self.ax.lines.remove(gpt.plot[0])
if len(gpt) > 1:
# delete single closest point from current group
# matplotlib coord to pixel coord, avoinding use of banker's round
y0, x0 = int(event.ydata + 0.5), int(event.xdata + 0.5)
distsq = [((p[1] - x0) ** 2 + (p[0] - y0) ** 2) for p in gpt.points]
# index and distance of smallest distance:
indexMin = min(enumerate(distsq), key=operator.itemgetter(1))
removedPt = gpt.points.pop(indexMin[0])
logger.info("x=%5.1f, y=%5.1f removed from group #%2s (%i points left)", removedPt[1], removedPt[0], gpt.label, len(gpt))
# annotate (new?) 1st point and add remaining points back
pt = (gpt.points[0][0], gpt.points[0][1])
gpt.annotate = annontate(pt, (pt[0] + 10, pt[1] + 10))
npl = numpy.array(gpt.points)
gpt.plot = self.ax.plot(npl[:, 1], npl[:, 0], "o", scalex=False, scaley=False)
elif len(gpt) == 1:
logger.info("Removing group #%2s containing 1 point", gpt.label)
gpt = self.points.pop(ring)
else:
logger.info("No groups to remove")
update_fig(self.fig)
sys.stdout.flush()
with self._sem:
logger.debug("Button: %i, Key modifier: %s", event.button, event.key)
if ((event.button == 3) and (event.key == 'shift')) or \
((event.button == 1) and (event.key == 'v')):
# if 'shift' pressed add nearest maximum to the current group
append_1_point(event)
elif ((event.button == 3) and (event.key == 'control')) or\
((event.button == 1) and (event.key == 'b')):
# if 'control' pressed add nearest maximum to a new group
single_point(event)
elif (event.button in [1, 3]) and (event.key == 'm'):
append_more_points(event)
elif (event.button == 3) or ((event.button == 1) and (event.key == 'n')):
# create new group
new_grp(event)
elif (event.key == "1") and (event.button in [1, 2]):
erase_1_point(event)
elif (event.button == 2) or (event.button == 1 and event.key == "d"):
erase_grp(event)
else:
logger.info("Unknown combination: Button: %i, Key modifier: %s", event.button, event.key)
def finish(self, filename=None, callback=None):
"""
Ask the ring number for the given points
:param filename: file with the point coordinates saved
"""
logging.info(os.linesep.join(self.help))
if not callback:
if not self.points.calibrant.dSpacing:
logger.error("Calibrant has no line ! check input parameters please, especially the '-c' option")
print(CALIBRANT_FACTORY)
raise RuntimeError("Invalid calibrant")
input("Please press enter when you are happy with your selection" + os.linesep)
# need to disconnect 'button_press_event':
self.fig.canvas.mpl_disconnect(self.mpl_connectId)
self.mpl_connectId = None
print("Now fill in the ring number. Ring number starts at 0, like point-groups.")
self.points.readRingNrFromKeyboard()
if filename is not None:
self.points.save(filename)
return self.points.getWeightedList(self.data)
else:
self.point_filename = filename
self.callback = callback
gui_utils.main_loop = True
# MAIN LOOP
pylab.show()
def contour(self, data, cmap="autumn", linewidths=2, linestyles="dashed"):
"""
Overlay a contour-plot
:param data: 2darray with the 2theta values in radians...
"""
if self.fig is None:
logging.warning("No diffraction image available => not showing the contour")
else:
while len(self.msp.images) > 1:
self.msp.images.pop()
while len(self.ct.images) > 1:
self.ct.images.pop()
while len(self.ct.collections) > 0:
self.ct.collections.pop()
tth_max = data.max()
tth_min = data.min()
if self.points.calibrant:
angles = [i for i in self.points.calibrant.get_2th()
if (i is not None) and (i >= tth_min) and (i <= tth_max)]
if not angles:
angles = None
else:
angles = None
try:
xlim, ylim = self.ax.get_xlim(), self.ax.get_ylim()
if not isinstance(cmap, matplotlib.colors.Colormap):
cmap = matplotlib.cm.get_cmap(cmap)
self.ct.contour(data, levels=angles, cmap=cmap, linewidths=linewidths, linestyles=linestyles)
self.ax.set_xlim(xlim)
self.ax.set_ylim(ylim)
print("Visually check that the overlaid dashed curve on the Debye-Sherrer rings of the image")
print("Check also for correct indexing of rings")
except MemoryError:
logging.error("Sorry but your computer does NOT have enough memory to display the 2-theta contour plot")
except ValueError:
logging.error("No contour-plot to display !")
update_fig(self.fig)
def massif_contour(self, data):
"""
Overlays a mask over a diffraction image
:param data: mask to be overlaid
"""
if self.fig is None:
logging.error("No diffraction image available => not showing the contour")
else:
tmp = 100 * numpy.logical_not(data)
mask = numpy.zeros((data.shape[0], data.shape[1], 4), dtype="uint8")
mask[:,:, 0] = tmp
mask[:,:, 1] = tmp
mask[:,:, 2] = tmp
mask[:,:, 3] = tmp
while len(self.msp.images) > 1:
self.msp.images.pop()
try:
xlim, ylim = self.ax.get_xlim(), self.ax.get_ylim()
self.msp.imshow(mask, cmap="gray", origin="lower", interpolation="nearest")
self.ax.set_xlim(xlim)
self.ax.set_ylim(ylim)
except MemoryError:
logging.error("Sorry but your computer does NOT have enough memory to display the massif plot")
update_fig(self.fig)
def closeGUI(self):
if self.fig is not None:
self.fig.clear()
self.fig = None
gc.collect()
def on_plus_pts_clicked(self, *args):
"""
callback function
"""
self.append_mode = True
print(self.append_mode)
def on_minus_pts_clicked(self, *args):
"""
callback function
"""
self.append_mode = False
print(self.append_mode)
def on_option_clicked(self, *args):
"""
callback function
"""
print("Option!")
def on_refine_clicked(self, *args):
"""
callback function
"""
print("refine, now!")
self.sb_action.setDisabled(True)
self.ref_action.setDisabled(True)
self.spinbox.setEnabled(False)
self.mpl_connectId = None
self.fig.canvas.mpl_disconnect(self.mpl_connectId)
pylab.ion()
if self.point_filename:
self.points.save(self.point_filename)
if self.callback:
self.callback(self.points.getWeightedList(self.data))
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