def compute_initial_figure(self):
ax = self.axes[0]
IMAGE_CACHE = util.ImageCache()
img = [IMAGE_CACHE.getVolume(fp) for fp in self.fullState.filePaths]
img0 = img[self.windowIndex - 1][0, ...]
img1 = img[self.windowIndex][0, ...]
img0 = gaussian(img0, .5)
img1 = gaussian(img1, .5)
img0 = self._simpleNorm(img0, 1.1)
img1 = self._simpleNorm(img1, 1.1)
p0Stack = img0.max(axis=0)**1.2
p1Stack = img1.max(axis=0)**1.2
p1Stack = skimgTransform.rotate(p1Stack, angle=0.85)
shift = np.array(
phase_cross_correlation(p0Stack,
p1Stack,
upsample_factor=1,
return_error=False))
dY, dX = int(round(shift[0])), int(round(shift[1]))
sliceY1, sliceY2 = self.buildSlices(dY, p1Stack.shape[0])
sliceX1, sliceX2 = self.buildSlices(dX, p1Stack.shape[1])
shifted = np.zeros(p1Stack.shape)
shifted[sliceY1, sliceX1] = p1Stack[sliceY2, sliceX2]
p1Stack = shifted
mergedStack = p0Stack
mergedStack = np.zeros((p0Stack.shape[0], p0Stack.shape[1], 3))
mergedStack[:, :, 0] = p0Stack
mergedStack[:, :, 1] = p1Stack
mergedStack[:, :, 2] = np.minimum(p0Stack, p1Stack)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
ax.set_aspect('equal')
ax.imshow(mergedStack)
import pandas as pd
import os
import sys
import pydynamo_brain.files as files
import pydynamo_brain.util as util
from pydynamo_brain.analysis import allTrees, allBranches, addedSubtractedTransitioned, allPuncta
from pydynamo_brain.analysis.neurom import neuroMAnalysisForNeurons
from pydynamo_brain.analysis.functions.tree import *
from pydynamo_brain.analysis.functions.branch import *
from pydynamo_brain.analysis.functions.puncta import *
from pydynamo_brain.model import FiloType
_IMG_CACHE = util.ImageCache()
# Either use a provided path, or open a filepicker to select one.
def usePathOrPick(path):
if path is not None:
return path
app = QtWidgets.QApplication([])
filePath, _ = QtWidgets.QFileDialog.getOpenFileName(
None, "Open dynamo save file", "", "Dynamo files (*.dyn.gz)")
return str(filePath)
# Example of running tree-based analysis
def runTreeAnalysis(path=None):
# List of analysis functions to produce answers across each tree: