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Feature/coherence matrix time axis clean #2

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6ba3312
`plot_coherence_matrix`: split image and matrix windows (#1493)
huchangyang May 29, 2026
7a8a22d
plot_coherence_matrix: add continuous time-axis view
huchangyang Jun 4, 2026
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8 changes: 6 additions & 2 deletions src/mintpy/cli/plot_coherence_matrix.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,12 @@ def create_parser(subparsers=None):
'Default: view.py img_file --wrap --noverbose')

# aux files
parser.add_argument('--tcoh', dest='tcoh_file', default='temporalCoherence.h5',
parser.add_argument('--tcoh', dest='tcoh_file',
help='temporal coherence file.')
parser.add_argument('-t','--template', dest='template_file',
help='temporal file.')
parser.add_argument('--time-axis', dest='time_axis', action='store_true',
help='Use continuous time axis instead of date indices for coherence matrix')

parser.add_argument('--save', dest='save_fig',
action='store_true', help='save the figure')
Expand All @@ -84,6 +86,8 @@ def cmd_line_parse(iargs=None):
mintpy_dir = os.path.dirname(os.path.dirname(inps.ifgram_file))
if not inps.img_file:
inps.img_file = os.path.join(mintpy_dir, 'velocity.h5')
if not inps.tcoh_file:
inps.tcoh_file = os.path.join(mintpy_dir, 'temporalCoherence.h5')
if not inps.template_file:
inps.template_file = os.path.join(mintpy_dir, 'smallbaselineApp.cfg')

Expand Down Expand Up @@ -114,7 +118,7 @@ def main(iargs=None):
obj = coherenceMatrixViewer(inps)
obj.open()
obj.plot()
obj.fig.canvas.mpl_disconnect(obj.cid)
#obj.fig_img.canvas.mpl_disconnect(obj.cid_img)


############################################################
Expand Down
172 changes: 134 additions & 38 deletions src/mintpy/plot_coherence_matrix.py
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
############################################################
# Program is part of MintPy #
# Copyright (c) 2013, Zhang Yunjun, Heresh Fattahi #
# Author: Zhang Yunjun, Nov 2018 #
# Author: Zhang Yunjun, Changyang Hu, Nov 2018 #
############################################################


Expand Down Expand Up @@ -62,16 +62,24 @@ class coherenceMatrixViewer():

def __init__(self, inps):
# figure variables
self.figname = 'Coherence matrix'
self.fig_size = None
self.fig = None
self.figname_img = 'Image'
self.figsize_img = None
self.fig_img = None
self.ax_img = None

self.figname_mat = 'Coherence Matrix'
self.figsize_mat = None
self.fig_mat = None
self.ax_mat = None

self.time_axis = getattr(inps, 'time_axis', False)

# copy inps to self object
for key, value in inps.__dict__.items():
setattr(self, key, value)

self._marker_artist = None


def open(self):
global vprint
Expand All @@ -89,11 +97,14 @@ def open(self):
self = read_network_info(self)

# auto figure size
if not self.fig_size:
if not self.figsize_img:
ds_shape = readfile.read(self.img_file)[0].shape
fig_size = pp.auto_figure_size(ds_shape, disp_cbar=True, scale=0.7)
self.fig_size = [fig_size[0]+fig_size[1], fig_size[1]]
vprint(f'create figure in size of {self.fig_size} inches')
self.figsize_img = pp.auto_figure_size(ds_shape, disp_cbar=True, scale=0.7)
vprint(f'create image figure in size of {self.figsize_img} inches')

if not self.figsize_mat:
self.figsize_mat = [8, 6]
vprint(f'create matrix figure in size of {self.figsize_mat} inches')

# read aux data
# 1. temporal coherence value
Expand All @@ -111,48 +122,109 @@ def open(self):


def plot(self):
# Figure 1
self.fig = plt.figure(self.figname, figsize=self.fig_size)
# Figure 1 - Image
self.fig_img, self.ax_img = plt.subplots(num=self.figname_img, figsize=self.figsize_img)
self.plot_init_image()

# Figure 2 - Coherence Matrix
self.fig_mat, self.ax_mat = plt.subplots(num=self.figname_mat, figsize=self.figsize_mat)
self.colormap = pp.ColormapExt(self.cmap_name, vlist=self.cmap_vlist).colormap
if all(i is not None for i in self.yx):
self.plot_coherence_matrix4pixel(self.yx)

# Axes 1 - Image
self.ax_img = self.fig.add_axes([0.05, 0.1, 0.4, 0.8])
# Link the canvas to the plots.
self.cid_img = self.fig_img.canvas.mpl_connect('button_press_event', self.update_coherence_matrix)

if self.disp_fig:
plt.show()
return

def plot_init_image(self):
"""Plot the initial image."""
view_cmd = self.view_cmd.format(self.img_file)
d_img, atr, view_inps = view.prep_slice(view_cmd)
self.coord = ut.coordinate(atr)

if all(i is not None for i in self.yx):
view_inps.pts_marker = 'r^'
view_inps.pts_yx = np.array(self.yx).reshape(-1, 2)

# point yx --> lalo for geocoded product
if 'Y_FIRST' in atr.keys():
view_inps.pts_lalo = np.array(
self.coord.radar2geo(
self.yx[0],
self.yx[1],
)[0:2],
).reshape(-1,2)

view_inps.print_msg = self.print_msg
self.ax_img = view.plot_slice(self.ax_img, d_img, atr, view_inps)[0]
self.fig_coord = view_inps.fig_coord

# Axes 2 - coherence matrix
self.ax_mat = self.fig.add_axes([0.55, 0.125, 0.40, 0.75])
self.colormap = pp.ColormapExt(self.cmap_name, vlist=self.cmap_vlist).colormap
if all(i is not None for i in self.yx):
self.plot_coherence_matrix4pixel(self.yx)
self.fig_img.canvas.manager.set_window_title(self.figname_img)
self.fig_img.tight_layout()
return

# Link the canvas to the plots.
self.cid = self.fig.canvas.mpl_connect('button_press_event', self.update_coherence_matrix)
if self.disp_fig:
plt.show()
def plot_coherence_matrix4pixel_time_axis(self, yx):
"""Plot coherence matrix with continuous time axis for one pixel."""
self.ax_mat.cla()

box = (yx[1], yx[0], yx[1]+1, yx[0]+1)
coh = readfile.read(self.ifgram_file, datasetName='coherence', box=box)[0]

ex_date12_list = self.ex_date12_list[:]
if self.min_coh_used > 0.:
ex_date12_list += np.array(self.date12_list)[coh < self.min_coh_used].tolist()
ex_date12_list = sorted(list(set(ex_date12_list)))

plotDict = {}
plotDict['fig_title'] = f'Y = {yx[0]}, X = {yx[1]}'
if self.tcoh is not None:
tcoh = self.tcoh[yx[0], yx[1]]
plotDict['fig_title'] += f', tcoh = {tcoh:.2f}'
plotDict['colormap'] = self.colormap
if len(self.cmap_vlist) >= 2:
plotDict['vlim'] = [self.cmap_vlist[0], self.cmap_vlist[-1]]
else:
plotDict['vlim'] = [0.0, 1.0]
plotDict['cbar_label'] = 'Coherence'
plotDict['disp_legend'] = False

pp.plot_coherence_matrix_time_axis(
self.ax_mat,
date12List=self.date12_list,
cohList=coh.tolist(),
date12List_drop=ex_date12_list,
p_dict=plotDict,
)

self.ax_mat.annotate('ifgrams\navailable', xy=(0.05, 0.05), xycoords='axes fraction', fontsize=12)
self.ax_mat.annotate('ifgrams\nused', ha='right', xy=(0.95, 0.85), xycoords='axes fraction', fontsize=12)

msg = f'pixel in yx = {tuple(yx)}, '
msg += f'min/max spatial coherence: {np.nanmin(coh):.2f} / {np.nanmax(coh):.2f}, '
if self.tcoh is not None:
msg += f'temporal coherence: {tcoh:.2f}'
vprint(msg)

self.fig_mat.canvas.manager.set_window_title(self.figname_mat)
if not hasattr(self, "_mat_tight_layout_done"):
self.fig_mat.tight_layout()
self._mat_tight_layout_done = True

self.fig_mat.canvas.draw_idle()
self.fig_mat.canvas.flush_events()

# plot/update marker on the image window
if self.fig_coord == 'geo':
lat, lon = self.coord.yx2lalo(yx[0], yx[1])
mx = lon if self.fig_coord == 'geo' else yx[1]
my = lat if self.fig_coord == 'geo' else yx[0]
if self._marker_artist is None:
self._marker_artist = self.ax_img.plot(
mx, my, 'r^', markersize=6, markeredgecolor='black'
)[0]
else:
self._marker_artist.set_data([mx], [my])

self.fig_img.canvas.draw_idle()
return

def plot_coherence_matrix4pixel(self, yx):
"""Plot coherence matrix for one pixel
Parameters: yx : list of 2 int
"""
if self.time_axis:
return self.plot_coherence_matrix4pixel_time_axis(yx)

self.ax_mat.cla()

# read coherence
Expand All @@ -169,7 +241,7 @@ def plot_coherence_matrix4pixel(self, yx):
plotDict = {}
plotDict['fig_title'] = f'Y = {yx[0]}, X = {yx[1]}'
# display temporal coherence value of the pixel
if self.tcoh_file:
if self.tcoh is not None:
tcoh = self.tcoh[yx[0], yx[1]]
plotDict['fig_title'] += f', tcoh = {tcoh:.2f}'
plotDict['colormap'] = self.colormap
Expand Down Expand Up @@ -198,17 +270,41 @@ def format_coord(x, y):

# info
msg = f'pixel in yx = {tuple(yx)}, '
if self.fig_coord == 'geo':
lat, lon = self.coord.yx2lalo(yx[0], yx[1])
msg += f'lat/lon = ({lat:.8f}, {lon:.8f}), '
msg += f'min/max spatial coherence: {np.min(coh):.2f} / {np.max(coh):.2f}, '
if self.tcoh_file:
if self.tcoh is not None:
msg += f'temporal coherence: {tcoh:.2f}'
vprint(msg)

self.fig_mat.canvas.manager.set_window_title(self.figname_mat)

# call tight_layout only once to avoid jitter and repeated work
if not hasattr(self, "_mat_tight_layout_done"):
self.fig_mat.tight_layout()
self._mat_tight_layout_done = True

# update figure
self.fig.canvas.draw_idle()
self.fig.canvas.flush_events()
self.fig_mat.canvas.draw_idle()
self.fig_mat.canvas.flush_events()

# plot/update marker on the image window
mx = lon if self.fig_coord == 'geo' else yx[1]
my = lat if self.fig_coord == 'geo' else yx[0]
if self._marker_artist is None:
self._marker_artist = self.ax_img.plot(
mx, my, 'r^', markersize=6, markeredgecolor='black'
)[0]
else:
self._marker_artist.set_data([mx], [my])

self.fig_img.canvas.draw_idle()

return

def update_coherence_matrix(self, event):
"""Update coherence matrix when clicking on either window."""
if event.inaxes == self.ax_img:
if self.fig_coord == 'geo':
yx = self.coord.lalo2yx(event.ydata, event.xdata)
Expand Down
28 changes: 22 additions & 6 deletions src/mintpy/plot_network.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ def plot_network(inps):
# figure names
ext = 'Ion.pdf' if os.path.basename(inps.file).startswith('ion') else '.pdf'
fig_names = {
'coherence' : [i+ext for i in ['pbaseHistory', 'coherenceHistory', 'coherenceMatrix', 'network']],
'coherence' : [i+ext for i in ['pbaseHistory', 'coherenceHistory', 'coherenceMatrix', 'coherenceMatrixTimeAxis', 'network']],
'offsetSNR' : [i+ext for i in ['pbaseHistory', 'SNRHistory', 'SNRMatrix', 'network']],
'tbase' : [i+ext for i in ['pbaseHistory', 'tbaseHistory', 'tbaseMatrix', 'network']],
'pbase' : [i+ext for i in ['pbaseHistory', 'pbaseRangeHistory', 'pbaseMatrix', 'network']],
Expand Down Expand Up @@ -204,7 +204,7 @@ def plot_network(inps):
)
if inps.save_fig:
fig.savefig(fig_names[1], **kwargs)
print(f'save figure to {fig_names[2]}')
print(f'save figure to {fig_names[1]}')

# Fig 3 - Coherence Matrix
fig_size3 = np.mean(inps.fig_size)
Expand All @@ -218,9 +218,25 @@ def plot_network(inps):
)[0]
if inps.save_fig:
fig.savefig(fig_names[2], **kwargs)
print(f'save figure to {fig_names[1]}')
print(f'save figure to {fig_names[2]}')

# Fig 4 - Coherence Matrix with Time Axis
fig_size4 = np.mean(inps.fig_size)
fig, ax = plt.subplots(figsize=[fig_size4, fig_size4])
ax = pp.plot_coherence_matrix_time_axis(
ax,
inps.date12List,
inps.cohList,
inps.date12List_drop,
p_dict=vars(inps),
)[0]
fig.tight_layout()
if inps.save_fig:
fig.savefig(fig_names[3], **kwargs)
print(f'save figure to {fig_names[3]}')

# Fig 4 - Interferogram Network
# Fig 5 - Interferogram Network (or Fig 4 if cohList is None)
fig_idx = 4 if inps.cohList is not None else 3
fig, ax = plt.subplots(figsize=inps.fig_size)
ax = pp.plot_network(
ax,
Expand All @@ -231,8 +247,8 @@ def plot_network(inps):
inps.date12List_drop,
)
if inps.save_fig:
fig.savefig(fig_names[3], **kwargs)
print(f'save figure to {fig_names[3]}')
fig.savefig(fig_names[fig_idx], **kwargs)
print(f'save figure to {fig_names[fig_idx]}')

if inps.disp_fig:
print('showing ...')
Expand Down
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