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Commit 480c350e authored by Andrey Aristov's avatar Andrey Aristov
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interactive plots

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src/napari_segment/_widget.py
+ 162
− 55
View file @ 480c350e
......@@ -9,6 +9,7 @@ Replace code below according to your needs.
from enum import Enum
import os
from functools import partial
from tempfile import TemporaryFile
import dask
import magicgui.widgets as w
......@@ -28,11 +29,14 @@ from scipy.ndimage import (
from functools import reduce
from skimage.measure import regionprops
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import (FigureCanvasQTAgg as FigureCanvas)
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure
import matplotlib
from threading import Thread
import logging
from importlib.metadata import PackageNotFoundError, version
import pandas as pd
try:
__version__ = version("napari-segment")
......@@ -41,9 +45,9 @@ except PackageNotFoundError:
__version__ = "Unknown"
logging.basicConfig(
level=logging.DEBUG, format="%(asctime)s %(levelname)s : %(message)s"
level=logging.WARNING, format="%(asctime)s %(levelname)s : %(message)s"
)
logger = logging.getLogger("napari_segment.widget")
logger = logging.getLogger("napari_segment._widget")
formatter = logging.Formatter(
"%(asctime)s - %(name)s - %(levelname)s : %(message)s"
......@@ -117,20 +121,26 @@ class ExampleQWidget(q.QWidget):
value=.9
)
self.btn = q.QPushButton("Save!")
self.btn = q.QPushButton("Save params!")
self.btn_save_csv = q.QPushButton("Save csv!")
self.check_auto_plot = w.CheckBox(label="Update Plots")
self.check_auto_plot.changed.connect(self.plot_stats)
self.canvas = FigureCanvas(Figure(figsize=(5,5)))
self.ax = self.canvas.figure.subplots(nrows=3, sharex=True)
self.ax = self.canvas.figure.subplots(nrows=3, sharex=False)
self.ax[0].set_title("Number of detections")
self.ax[1].set_title(diams_title := "Diameters")
self.diams_title = diams_title
self.ax[2].set_title("Eccentricities")
self.canvas.figure.tight_layout()
self._count, = self.ax[0].plot(range(10), [0]*10)
self._diams, = self.ax[1].plot(range(10), [0]*10)
self._eccs, = self.ax[2].plot(range(10), [0]*10)
self._count, = self.ax[0].plot(range(10), [0]*10, "o", picker=True, pickradius=5)
self._diams, = self.ax[1].plot(range(10), [0]*10, "o", picker=True, pickradius=5)
self._eccs, = self.ax[2].plot(range(10), [0]*10, "o", picker=True, pickradius=5)
self.container = w.Container(
label="Container",
widgets=[
self.input,
w.Label(label="Prepocessing"),
......@@ -144,6 +154,7 @@ class ExampleQWidget(q.QWidget):
self.min_diam,
self.max_diam,
self.max_ecc,
self.check_auto_plot
]
)
......@@ -151,27 +162,46 @@ class ExampleQWidget(q.QWidget):
self.layout().addWidget(self.container.native)
self.layout().addWidget(self.btn)
self.layout().addWidget(self.canvas)
self.layout().addWidget(NavigationToolbar(self.canvas, self))
self.layout().addWidget(self.btn_save_csv)
self.layout().addStretch()
self.viewer.layers.events.inserted.connect(self.reset_choices)
self.viewer.layers.events.removed.connect(self.reset_choices)
self.input.changed.connect(self.restore_params)
self.input.changed.connect(self.preprocess)
self.binning_widget.changed.connect(self.preprocess)
self.thr.changed.connect(self.threshold)
self.erode.changed.connect(self.threshold)
self.use.changed.connect(self.preprocess)
self.smooth.changed.connect(self.preprocess)
self.min_diam.changed.connect(self.update_out)
self.max_diam.changed.connect(self.update_out)
self.max_ecc.changed.connect(self.update_out)
self.btn.clicked.connect(self.save_params)
self.canvas.mpl_connect('button_press_event', self.onfigclick)
self.canvas.mpl_connect('pick_event', self.on_pick)
logger.debug("Initialization finished.")
if (choice := self.input.current_choice):
if self.input.current_choice:
self.restore_params()
self.preprocess()
def move_step(self, slice):
cur_ = self.viewer.dims.current_step
new_ = list(cur_)
new_[0] = slice
self.viewer.dims.current_step = tuple(new_)
def onfigclick(self, event):
print('%s click: button=%d, x=%d, y=%d, xdata=%f, ydata=%f' %
('double' if event.dblclick else 'single', event.button,
event.x, event.y, event.xdata, event.ydata))
self.move_step(np.round(event.xdata, 0).astype(int))
def on_pick(self, event):
line = event.artist
xdata, ydata = line.get_data()
ind = event.ind
print(f'on pick line: {np.array([xdata[ind], ydata[ind]]).T}')
self.move_step(xdata[ind])
def _invert(self, data2D):
return 1 - norm01(gaussian_filter(data2D, self.smooth.value))
......@@ -185,7 +215,17 @@ class ExampleQWidget(q.QWidget):
)
def preprocess(self):
if not self.input.current_choice:
return
logger.debug(f"start preprocessing {self.input.current_choice}")
try:
self.path = self.viewer.layers[self.input.current_choice].metadata[
"path"
]
except KeyError:
self.path = ""
self.binning = self.binning_widget.value
try:
self.data = self.viewer.layers[self.input.current_choice].data[
......@@ -197,7 +237,8 @@ class ExampleQWidget(q.QWidget):
return
try:
self.pixel_size = self.viewer.layers[self.input.current_choice].metadata["pixel_size_um"]
self.pixel_size = self.viewer.layers[self.input.current_choice]\
.metadata["pixel_size_um"]
self.unit = "um"
except KeyError:
......@@ -258,18 +299,21 @@ class ExampleQWidget(q.QWidget):
**{"name": name, "scale": self.scale},
)
else:
logger.debug(f'Updating Preprocessing layer with {self.smooth_gradient}')
logger.debug(f'Updating Preprocessing layer with \
{self.smooth_gradient}')
self.viewer.layers[name].data = self.smooth_gradient
self.viewer.layers[name].scale = self.scale
logger.debug(f'Preprocessing finished, sending {self.smooth_gradient} to thresholding')
logger.debug(f'Preprocessing finished, \
sending {self.smooth_gradient} to thresholding')
self.threshold()
def threshold(self):
logger.debug('Start thresholding step')
if not self.input.current_choice:
return
logger.debug(f'Thresholding with the thr={self.thr.value} and erode={self.erode.value}')
logger.debug(f'Thresholding with the thr={self.thr.value} \
and erode={self.erode.value}')
self.labels = self.smooth_gradient.map_blocks(
partial(
threshold_gradient, thr=self.thr.value, erode=self.erode.value
......@@ -283,13 +327,15 @@ class ExampleQWidget(q.QWidget):
opacity=0.3,
**{"name": name, "scale": self.scale},
)
self.viewer.layers[name].contour = 8 // self.binning
else:
logger.debug(f'Updating Detections layer with {self.labels}')
self.viewer.layers[name].data = self.labels
self.viewer.layers[name].scale = self.scale
self.viewer.layers[name].contour = 8 / self.binning
logger.debug(f'Thresholding succesful. Sending labels {self.labels} to filtering')
logger.debug(f'Thresholding succesful. \
Sending labels {self.labels} to filtering')
self.update_out()
def update_out(self):
......@@ -298,8 +344,9 @@ class ExampleQWidget(q.QWidget):
return
logger.debug(f'Start filtering')
try:
logger.debug(f"""Filtering labels by ({self.min_diam.value / self.binning}
< size[px] < {self.max_diam.value / self.binning})
logger.debug(f"""Filtering labels by \
({self.min_diam.value / self.binning} \
< size[px] < {self.max_diam.value / self.binning}) \
and eccentricity > {self.max_ecc.value}""")
selected_labels = dask.array.map_blocks(
......@@ -310,6 +357,8 @@ class ExampleQWidget(q.QWidget):
self.max_ecc.value,
dtype=np.int32,
)
self.selected_labels = selected_labels
if not (name := "selected labels") in self.viewer.layers:
logger.debug(f'No selected labels layer found, adding one')
......@@ -320,7 +369,7 @@ class ExampleQWidget(q.QWidget):
**{"name": name, "scale": self.scale},
)
else:
logger.debug(f'Updating selected labels layer with {selected_labels}')
logger.debug(f'Updating labels layer with {selected_labels}')
self.viewer.layers[name].scale = self.scale
self.viewer.layers[name].data = selected_labels
......@@ -331,40 +380,75 @@ class ExampleQWidget(q.QWidget):
show_error(f"Relax filter! {e}")
try:
self.plot_stats(selected_labels)
self.plot_stats()
except Exception as e:
show_error(f"Plot failed: {e}")
def plot_stats(self, data):
props = [regionprops(label_image=img) for img in data.compute()]
def plot_stats(self, ignore_check_auto_plot=False):
if not self.check_auto_plot.value:
if not ignore_check_auto_plot:
return
props = [regionprops(label_image=img) for img in self.selected_labels.compute()]
num_regions_per_frame = [len(p) for p in props]
diams_ = [
area_ = [
[
(i, prop.major_axis_length * self.binning * self.pixel_size) \
(i, prop.area * (self.binning * self.pixel_size)**2) \
for prop in props_per_frame
] for i,props_per_frame in enumerate(props)
]
diams = reduce(lambda a,b: a+b, diams_[:])
area = reduce(lambda a,b: a+b, area_[:])
self.props_df = \
pd.DataFrame(
data=area,
columns=["frame", (area_col := f"area [{self.unit}$^2$]")]
)
self.props_df.loc[:, (diam_col := f"diameter [{self.unit}]")] = \
np.sqrt(self.props_df[area_col]) * 2 / np.pi
eccs_ = [
[
(i, prop.eccentricity) for prop in props_per_frame
(prop.eccentricity) for prop in props_per_frame
] for i,props_per_frame in enumerate(props)
]
eccs = reduce(lambda a,b: a+b, eccs_)
self.props_df.loc[:, (ecc_col := "eccentricity")] = eccs
data=self.props_df
self._count.set_data(*zip(*enumerate(num_regions_per_frame)))
self._diams.set_data(*zip(*diams))
self._eccs.set_data(*zip(*eccs))
[a.set_xlim(len(num_regions_per_frame)) for a in self.ax]
self.ax[0].set_ylim(min(num_regions_per_frame), max(num_regions_per_frame))
self.ax[1].set_ylim(min(r := [d[1] for d in diams]), max(r))
self._diams.set_data(data["frame"], data[diam_col])
self._eccs.set_data(data["frame"], data[ecc_col])
[a.set_xlim(0, len(num_regions_per_frame)) for a in self.ax]
self.ax[0].set_ylim(0, max(num_regions_per_frame) + 1)
self.ax[1].set_ylim(
self.props_df[diam_col].min(),
self.props_df[diam_col].max()
)
self.ax[2].set_ylim(0,1)
self.canvas.draw_idle()
def save_csv(self):
self.plot_stats(ignore_check_auto_plot=True)
try:
len(self.props_df)
except Exception as e:
logger.error(f"Unable to find the data to save: {e}")
show_error(f"Unable to find the data to save: {e}")
return
path = self.path + ".table.csv"
try:
self.props_df.to_csv(path)
logger.info(f"Saved csv {path}")
show_info(f"Saved csv {path}")
except Exception as e:
logger.error(f"Error saving csv: {e}")
show_error(f"Error saving csv: {e}")
def save_params(self):
data = {
......@@ -378,27 +462,33 @@ class ExampleQWidget(q.QWidget):
"max_ecc": self.max_ecc.value,
}
try:
path = self.viewer.layers[self.input.current_choice].metadata[
"path"
]
dir = os.path.dirname(path)
filename = os.path.basename(path)
dir = os.path.dirname(self.path)
filename = os.path.basename(self.path)
new_name = filename + ".params.yaml"
with open(os.path.join(dir, new_name), "w") as f:
yaml.safe_dump(data, f)
show_info(f"Parameters saves into {new_name}")
except KeyError:
show_error("Saving parameters failed")
logger.info(f"Parameters saves into {new_name}")
except Exception as e:
show_error(f"Saving parameters into {new_name} failed: {e}")
logger.error(f"Saving parameters into {new_name} failed: {e}")
with open((ff := ".latest.params.yaml"), "w") as f:
yaml.safe_dump(data, f)
show_info(f"Parameters saves into {ff}")
logger.info(f"Parameters saves into {ff}")
def restore_params(self):
logger.debug(f'Start restoring parameters')
try:
path = self.viewer.layers[self.input.current_choice].metadata[
self.path = self.viewer.layers[self.input.current_choice].metadata[
"path"
]
except KeyError:
self.path = ""
try:
path = self.path
dir = os.path.dirname(path)
filename = os.path.basename(path)
new_name = filename + ".params.yaml"
......@@ -408,6 +498,7 @@ class ExampleQWidget(q.QWidget):
with open(ppp := os.path.join(dir, new_name)) as f:
data = yaml.safe_load(f)
show_info(f"restoring parameters from {new_name}")
logger.info(f"restoring parameters from {new_name}")
except (UnboundLocalError, UnicodeDecodeError, FileNotFoundError):
try:
......@@ -416,7 +507,7 @@ class ExampleQWidget(q.QWidget):
show_info(f"restoring parameters from {ppp}")
except FileNotFoundError:
return
print(data)
logger.debug(f'Loaded parameters: {data}')
try:
self.binning_widget.value = data["binning"]
self.use.value = data["use"]
......@@ -428,16 +519,32 @@ class ExampleQWidget(q.QWidget):
self.max_ecc.value = data["max_ecc"]
except Exception as e:
show_error(f"Restore settings failed, {e}")
logger.error(f"Restore settings failed, {e}")
self.binning_widget.changed.connect(self.preprocess)
self.thr.changed.connect(self.threshold)
self.erode.changed.connect(self.threshold)
self.use.changed.connect(self.preprocess)
self.smooth.changed.connect(self.preprocess)
self.min_diam.changed.connect(self.update_out)
self.max_diam.changed.connect(self.update_out)
self.max_ecc.changed.connect(self.update_out)
self.btn.clicked.connect(self.save_params)
self.btn_save_csv.clicked.connect(self.save_csv)
def reset_choices(self, event=None):
self.input.reset_choices(event)
self.input.choices = [
logger.debug(f"New layer added. Reset choices. Event: {event}")
new_layers = [
layer.name
for layer in self.viewer.layers
if isinstance(layer, Image) and layer.name != "Preprocessing"
]
# self.restore_params()
if self.input.choices != new_layers:
self.input.choices = new_layers
logger.debug(f'Updating layer list with {new_layers}')
else:
logger.debug('No new data layers, probably added pipeline layers triggered this reset')
def norm01(data):
d = data.copy()
......
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