def makeDetachfigure(self):
if hasattr(self, 'figure4'):
pass
else:
self.figure4 = Figure()
self.canvas4 = FigCanvas(self.figure4)
self.ax4 = self.figure4.add_subplot(111)
if hasattr(self, 'figure5'):
pass
else:
self.ax4 = self.figure4.add_subplot(111)
self.figure5 = Figure()
self.canvas5 = FigCanvas(self.figure5)
self.ax5 = self.figure5.add_subplot(111)
self.detach_plot_TT()
def plot_raw_dataset_um(
points_um,
savedir='',
title='images',
grid=(3, 3),
figsize=(8, 8),
size=0.1,
dpi=300,
invert_yaxis=True,
):
'''
Plot the mRNA spots for each gene.
'''
print('Plotting mRNA spots of selected genes...')
if not os.path.exists(savedir):
os.makedirs(savedir)
genes_per_plot = grid[0] * grid[1]
num_plots, remain = divmod(len(points_um), genes_per_plot)
if remain != 0:
num_plots += 1
gene_list = list(points_um.keys())
gene_idx = 0
for plot_num in range(num_plots):
fig = Figure(figsize=figsize, dpi=dpi)
canvas = FigCanvas(fig)
fig.set_canvas(canvas)
for gridpos in range(genes_per_plot):
if gene_idx == len(points_um):
break
ax = fig.add_subplot(grid[0], grid[1], gridpos + 1)
ax.scatter(
points_um[gene_list[gene_idx]][:, 1],
points_um[gene_list[gene_idx]][:, 0],
s=size,
)
ax.set_aspect('equal')
ax.set_title(gene_list[gene_idx])
if invert_yaxis:
ax.invert_yaxis()
gene_idx += 1
fig.suptitle(title + f'\n {plot_num + 1} of {num_plots}')
fig.tight_layout(rect=(0, 0, 1, .94))
savename = (
f'raw_image_{plot_num+1}_{datetime.now().strftime("%Y%m%d_%H%M%S")}.png'
)
fig.savefig(os.path.join(savedir, savename), dpi=dpi)
canvas.close()
fig.clear()
plt.close()
def __init__(self):
super(PlotWindow, self).__init__()
self.figure = plt.figure()
self.canvas = FigCanvas(self.figure)
self.toolbar = Navbar(self.canvas, self)
layout = QVBoxLayout()
layout.addWidget(self.canvas)
layout.addWidget(self.toolbar)
self.setLayout(layout)
self.show()
def initUI(self):
QMainWindow().setCentralWidget(QWidget())
self.setLayout(QVBoxLayout())
self.layout().setContentsMargins(0, 0, 0, 0)
self.layout().setSpacing(0)
canvas = FigCanvas(self.fig)
canvas.draw()
scroll = QScrollArea(self)
scroll.setWidget(canvas)
nav = NabToolbar(canvas, self)
self.layout().addWidget(nav)
self.layout().addWidget(scroll)
self.show_basic()
def plotALot(
self,
gene_list, # list of genes to plot
savedir="",
title="images",
grid=(4, 8), # grid to plot for each figure
figsize=(16, 9),
dpi=300,
):
"""
plot a lot of intensity maps
from a list of genes
"""
genes_per_plot = grid[0] * grid[1]
num_plots, remainder = divmod(len(gene_list), (genes_per_plot))
# add an extra plot if
# number of genes is not perfectly divisible by number of plots
if remainder != 0:
num_plots += 1
for img_num in range(len(self.img_arrays)):
# set up index for number of genes already plotted
# ------------------------------------------------
reordered_idx = 0
for plot_num in range(num_plots):
# set up figure canvas
# --------------------
fig = Figure(figsize=figsize, dpi=dpi)
canvas = FigCanvas(fig)
fig.set_canvas(canvas)
for gridpos in range(genes_per_plot):
# check if we have reached end of gene list
# -----------------------------------------
if reordered_idx == len(gene_list) - 1:
break
# create temporary axes reference
# -------------------------------
ax = fig.add_subplot(grid[0], grid[1], gridpos + 1)
# plot the current gene
# ---------------------
array_idx = self.gene_index_dict[gene_list[reordered_idx]]
ax.imshow(self.img_arrays[img_num][array_idx, ...],
cmap="hot")
ax.set_title(gene_list[reordered_idx])
# increment gene index
# --------------------
reordered_idx += 1
fig.suptitle(title + f"\n{self.hdf5_file_list[img_num]}"
f"\n({plot_num + 1} of {num_plots})")
fig.tight_layout(rect=(0, 0, 1, .94))
# save the plot
# -------------
savename = (
f"image_{img_num + 1}_{title.replace(' ','_')}"
f"_{plot_num + 1}of{num_plots}_{self.time_str}.png")
if not os.path.exists(savedir):
os.mkdir(savedir)
fig.savefig(os.path.join(savedir, savename), dpi=dpi)
# close the canvas
# ----------------
canvas.close()
fig.clear()
def plotALot(
img_array,
gene_index_dict, # list of genes to plot
reordered_genes=None,
savedir="",
title="images",
grid=(3, 6), # grid to plot for each figure
figsize=(16, 9),
dpi=300,
):
"""
plot a lot of images from a list of genes
"""
genes_per_plot = grid[0] * grid[1]
num_plots, remainder = divmod(len(gene_index_dict), (genes_per_plot))
# add an extra plot if
# number of genes is not perfectly divisible by number of plots
if remainder != 0:
num_plots += 1
if reordered_genes is None:
reordered_genes = [
None,
] * len(gene_index_dict)
for gene in gene_index_dict:
reordered_genes[gene_index_dict[gene]["index"]] = gene
# set up index for number of genes already plotted
# ------------------------------------------------
array_idx = 0
for plot_num in range(num_plots):
# set up figure canvas
# --------------------
fig = Figure(figsize=figsize, dpi=dpi)
canvas = FigCanvas(fig)
fig.set_canvas(canvas)
for gridpos in range(genes_per_plot):
# check if we have reached end of gene list
# -----------------------------------------
if array_idx == len(gene_index_dict):
break
# create temporary axes reference
# -------------------------------
ax = fig.add_subplot(grid[0], grid[1], gridpos + 1)
# plot the current gene (array_idx)
# ---------------------
gene = reordered_genes[array_idx]
ax.imshow(img_array[gene_index_dict[gene]["index"], ...],
cmap="hot")
ax.set_title(gene)
ax.grid(False)
# increment gene index
# --------------------
array_idx += 1
fig.suptitle(title + f" ({plot_num + 1} of {num_plots})")
fig.tight_layout(rect=(0, 0, 1, .94))
# save the plot
# time_now = datetime.datetime.now().strftime("%Y%m%d_%H%M")
savename = (f"{title.replace(' ','_')}"
f"_{plot_num + 1}of{num_plots}.png")
if not os.path.exists(savedir):
os.mkdir(savedir)
fig.savefig(os.path.join(savedir, savename), dpi=dpi)
canvas.close()
fig.clear()
def __init__(self):
# Inheritage from the base/super class
super(self.__class__, self).__init__()
self.setupUi(self)
self.icon2 = QIcon()
self.icon2.addPixmap(QPixmap(resource_path("SimPel_icon.ico")))
self.setWindowIcon(self.icon2)
self.versionnumber = '1.0.0'
# Customized QWidgets as containing matplotlib figure instances
self.figure = Figure()
self.figure.set_facecolor('white')
self.canvas = FigCanvas(self.figure)
self.layout = QVBoxLayout(self.widgetplot)
self.layout.addWidget(self.canvas)
self.ax = self.figure.add_subplot(111)
self.ax.set_yticks([])
self.ax.set_xticks([])
self.figure2 = Figure()
self.figure2.set_facecolor('white')
self.canvas2 = FigCanvas(self.figure2)
self.layout2 = QVBoxLayout(self.Distancedistrwindow)
self.layout2.addWidget(self.canvas2)
self.ax2 = self.figure2.add_subplot(111)
self.ax2.set_yticks([])
self.ax2.set_xticks([])
self.figure3 = Figure()
self.figure3.set_facecolor('white')
self.canvas3 = FigCanvas(self.figure3)
self.layout3 = QVBoxLayout(self.FTwindow)
self.layout3.addWidget(self.canvas3)
self.ax3 = self.figure3.add_subplot(111)
self.ax3.set_yticks([])
self.ax3.set_xticks([])
self.toolbar = Navi(self.canvas, self)
self.toolbar.hide()
# Initialize all parameters
initialize(self)
self.configs = configs
self.configs_str = configs_str
self.configs_lim_min = configs_lim_min
self.configs_lim_max = configs_lim_max
# ALL SIGNAL/SLOT CONNECTIONS
self.Startbutton.clicked.connect(self.make_calculation)
self.zoomButtonPeldorTT.clicked.connect(self.zoominPELDORTT)
self.panPELDORTT.clicked.connect(self.makepanPELDORTT)
self.DetachButton.clicked.connect(self.makeDetachfigure)
self.Distance1edit.textChanged.connect(
lambda: self.read_dist(self.Distance1edit.text(), 0))
self.Distance2edit.textChanged.connect(
lambda: self.read_dist(self.Distance2edit.text(), 1))
self.Distance3edit.textChanged.connect(
lambda: self.read_dist(self.Distance3edit.text(), 2))
self.Distance4edit.textChanged.connect(
lambda: self.read_dist(self.Distance4edit.text(), 3))
self.Distance5edit.textChanged.connect(
lambda: self.read_dist(self.Distance5edit.text(), 4))
self.Coeff1edit.textChanged.connect(
lambda: self.read_coeff(self.Coeff1edit.text(), 0))
self.Coeff2edit.textChanged.connect(
lambda: self.read_coeff(self.Coeff2edit.text(), 1))
self.Coeff3edit.textChanged.connect(
lambda: self.read_coeff(self.Coeff3edit.text(), 2))
self.Coeff4edit.textChanged.connect(
lambda: self.read_coeff(self.Coeff4edit.text(), 3))
self.Coeff5edit.textChanged.connect(
lambda: self.read_coeff(self.Coeff5edit.text(), 4))
self.Standard1.textChanged.connect(
lambda: self.read_sigmas(self.Standard1.text(), 0))
self.Standard2.textChanged.connect(
lambda: self.read_sigmas(self.Standard2.text(), 1))
self.Standard3.textChanged.connect(
lambda: self.read_sigmas(self.Standard3.text(), 2))
self.Standard4.textChanged.connect(
lambda: self.read_sigmas(self.Standard4.text(), 3))
self.Standard5.textChanged.connect(
lambda: self.read_sigmas(self.Standard5.text(), 4))
self.Timescalebox.valueChanged.connect(self.set_stepsize)
self.Timescalebox.lineEdit().setReadOnly(True)
self.Timescaleedit.textChanged.connect(self.read_timescale)
self.Moddepthedit.textChanged.connect(self.read_moddpeth)
self.Bgdecayedit.textChanged.connect(self.read_bgdecy)
self.BgDimbox.valueChanged.connect(self.set_bgdim)
self.BgDimbox.lineEdit().setReadOnly(True)
self.EnableBgButton.toggled.connect(
lambda: self.btn1state(self.EnableBgButton))
self.ShowBGButton.toggled.connect(
lambda: self.btn2state(self.ShowBGButton))
self.Sigmaedit.textChanged.connect(self.read_sigma)
self.Universal_standard_dev_button.toggled.connect(
lambda: self.use_universal_sigma(self.Universal_standard_dev_button
))
self.EnableNoiseButton.toggled.connect(
lambda: self.btn3state(self.EnableNoiseButton))
self.SNR_edit.textChanged.connect(self.read_SNR)
self.Checkbox_superadaptive.stateChanged.connect(
lambda: self.use_superadaptive_Gaussian(self.Checkbox_superadaptive
))
self.ButtonFullyAdaptive.toggled.connect(
lambda: self.btn5state(self.ButtonFullyAdaptive))
self.fresnelbutton.toggled.connect(
lambda: self.btn7state(self.fresnelbutton))
self.User_defined_distr.toggled.connect(
lambda: self.Userdef_Dist(self.User_defined_distr))
self.Load_experimental_button.clicked.connect(self.open_file_TT)
self.Configurations.clicked.connect(self.open_config)
self.Loadbutton_User_def.clicked.connect(self.open_file)
self.Savebutton.clicked.connect(self.save_file)
self.Closebutton.clicked.connect(self.close_GUI)
def compare_kde_level(
kde_files,
savedir='.',
title='plot',
grid=(2, 2),
figsize=(8, 8),
dpi=300,
# invert_yaxis=True,
xlim=None,
ylim=None,
):
'''
Zooming in a particular case to select the proper KDE smoothing level.
- kde_files: a dictionary of kde result for comparison;
key: kde_level
value: kde_file_name
- savedir, samename: the output plot
- xlim, ylim: the zooming region
'''
if not os.path.exists(savedir):
os.makedirs(savedir)
kde_per_plot = grid[0] * grid[1]
num_plots, remain = divmod(len(kde_files), kde_per_plot)
if remain != 0:
num_plots += 1
kde_list = list(kde_files.keys())
kde_idx = 0
for plot_num in range(num_plots):
fig = Figure(figsize=figsize, dpi=dpi)
canvas = FigCanvas(fig)
fig.set_canvas(canvas)
for gridpos in range(kde_per_plot):
if kde_idx == len(kde_files):
break
kde = kde_list[kde_idx]
kde_file = kde_files[kde]
array_kde = np.load(kde_file)
# KDE files naming convention (example): pdf_sd1_bw2_GENE.npy
ax = fig.add_subplot(grid[0], grid[1], gridpos + 1)
ax.imshow(array_kde[:, :, 0], aspect='equal')
scalebar = ScaleBar(1, 'um', pad=0.2, font_properties={'size': 12})
ax.add_artist(scalebar)
if xlim is not None:
ax.set_xlim(xlim)
if ylim is not None:
ax.set_ylim(ylim)
# if invert_yaxis:
# ax.invert_yaxis()
ax.set_title(f'kde = {kde}')
kde_idx += 1
fig.suptitle(f'{title}_{plot_num+1}/{num_plots}')
fig.tight_layout(rect=(0, 0, 1, 0.9))
savename = (f'{title}_{plot_num+1}_'
f'{datetime.now().strftime("%Y%m%d_%H%M%S")}.png')
fig.savefig(os.path.join(savedir, savename), dpi=dpi)
canvas.close()
fig.clear()
return True