def test_writeToNavFile():
coords = [
(2149, 1904),
(2637, 1448),
(1732, 1229),
(2239, 1535),
(2293, 2128),
(2897, 1120),
(2111, 2088),
(1769, 1044),
(2819, 1488),
(2019, 1680),
(2095, 1311),
(2598, 1633),
]
coords = [Pt(*coord) for coord in coords]
mapID = "30-A"
nav = openNavfile("nav.nav")
options = NavOptions(
groupOption=0,
groupRadius=123,
pixelSize=1,
numGroups=1,
ptsPerGroup=8,
acquire=1,
)
navPts = ptsToNavPts(coords, nav, mapID, startLabel=9000, options=options)
newNavData = "AdocVersion = 2.00\n\n" + "".join(str(pt) for pt in navPts)
with open("newNav.nav", "w") as f:
f.write(newNavData)
with open("newNav_validate.nav") as f:
validationData = f.read()
assert validationData == newNavData
def _selectGroupOption(self, groupOption):
global navOptions
navOptions = NavOptions(
groupOption,
navOptions.groupRadius,
navOptions.pixelSize,
navOptions.numGroups,
navOptions.ptsPerGroup,
navOptions.acquire,
)
if groupOption == 1: # groups by radius
self.groupRadiusLabel.show()
self.groupRadiusLineEdit.show()
self.groupRadiusLabelµm.show()
self.pixelSizeLabel.show()
self.pixelSizeLineEdit.show()
self.pixelSizeLabelnm.show()
self.numGroupsLabel.hide()
self.numGroupsSB.hide()
self.ptsPerGroupLabel.hide()
self.ptsPerGroupSB.hide()
elif groupOption == 3: # numGroups
self.groupRadiusLabel.hide()
self.groupRadiusLineEdit.hide()
self.groupRadiusLabelµm.hide()
self.pixelSizeLabel.hide()
self.pixelSizeLineEdit.hide()
self.pixelSizeLabelnm.hide()
self.numGroupsLabel.show()
self.numGroupsSB.show()
self.ptsPerGroupLabel.hide()
self.ptsPerGroupSB.hide()
elif groupOption == 4: # ptsPerGroup
self.groupRadiusLabel.hide()
self.groupRadiusLineEdit.hide()
self.groupRadiusLabelµm.hide()
self.pixelSizeLabel.hide()
self.pixelSizeLineEdit.hide()
self.pixelSizeLabelnm.hide()
self.numGroupsLabel.hide()
self.numGroupsSB.hide()
self.ptsPerGroupLabel.show()
self.ptsPerGroupSB.show()
else:
self.groupRadiusLabel.hide()
self.groupRadiusLineEdit.hide()
self.groupRadiusLabelµm.hide()
self.pixelSizeLabel.hide()
self.pixelSizeLineEdit.hide()
self.pixelSizeLabelnm.hide()
self.numGroupsLabel.hide()
self.numGroupsSB.hide()
self.ptsPerGroupLabel.hide()
self.ptsPerGroupSB.hide()
self.repaint()
def _setPtsPerGroup(self, ptsPerGroup):
global navOptions
navOptions = NavOptions(
navOptions.groupOption,
navOptions.groupRadius,
navOptions.pixelSize,
navOptions.numGroups,
ptsPerGroup,
navOptions.acquire,
)
self.ptsPerGroupSB.setValue(navOptions.ptsPerGroup)
def saveAndQuit(self):
global navOptions
navOptions = NavOptions(
navOptions.groupOption,
navOptions.groupRadius,
navOptions.pixelSize,
navOptions.numGroups,
navOptions.ptsPerGroup,
int(self.cbAcquire.isChecked()),
)
global pts
global finalPts
finalPts = pts
self.parentWidget().parentWidget().writeSettings()
QApplication.quit()
def _setPixelSize(self, s: str):
try:
pixelSize = float("{:.1f}".format(float(s))) # in nm
self.pixelSizeLineEdit.setText(str(pixelSize))
except Exception as e:
print("_setPixelSize exception")
print(e)
pixelSize = None
global navOptions
navOptions = NavOptions(
navOptions.groupOption,
navOptions.groupRadius,
pixelSize,
navOptions.numGroups,
navOptions.ptsPerGroup,
navOptions.acquire,
)
def _setGroupRadius(self, s: str):
try:
groupRadius = float("{:.1f}".format(float(s)))
self.groupRadiusLineEdit.setText(str(groupRadius))
except Exception as e:
print("_setGroupRadius exception")
print(e)
groupRadius = None
global navOptions
navOptions = NavOptions(
navOptions.groupOption,
groupRadius,
navOptions.pixelSize,
navOptions.numGroups,
navOptions.ptsPerGroup,
navOptions.acquire,
)
def main():
import argparse
import sys
import imageio
from semmatch.core import (
Pt,
NavOptions,
templateMatch,
imresize,
houghCircles,
laceySearch,
)
from semmatch.autodoc import ptsToNavPts, createAutodoc, openNavfile
from semmatch.groups import getRandPts
parser = argparse.ArgumentParser(
description="template matching tool for SerialEM")
# required
parser.add_argument("--navfile", help="SerialEM nav file", required=True)
parser.add_argument("--image", help="jpg", required=True)
parser.add_argument("--mapLabel", help="label id", required=True)
parser.add_argument("--newLabel",
help="starting label of added points",
type=int,
required=True)
parser.add_argument("-o",
"--output",
help="output nav file",
required=True)
# optional
parser.add_argument("--gui",
help="interactive gui mode",
action="store_true")
parser.add_argument("--template",
help="template image to use; required in non-gui mode")
parser.add_argument("--houghCircles",
help="automatic detection for holey grid",
action="store_true")
parser.add_argument("--param2",
help="threshold for houghCircles",
type=int,
default=60)
parser.add_argument("--pixelSize",
help="pixelSize in nm",
type=float,
required=True)
parser.add_argument("--laceySearch",
help="automatic detection for lacey grid",
action="store_true")
parser.add_argument(
"--laceyThreshLow",
help="lower threshold for laceySearch",
type=int,
default=195,
)
parser.add_argument(
"--laceyThreshHigh",
help="upper threshold for laceySearch",
type=int,
default=245,
)
parser.add_argument(
"--maxPts",
help="limit number of pts found via houghCircles or laceySearch",
type=int,
)
parser.add_argument(
"--groupOption",
help="grouping option for points;" + "0 = no groups; " +
"1 = groups based on radius (requires --groupRadius and --pixelSize);"
+ "2 = all points as one group;" + "3 = specify number of groups;" +
"4 = specify number of points per group",
type=int,
default=0,
)
parser.add_argument("--threshold",
help="threshold value for zncc",
type=float,
default=0.8)
parser.add_argument("--reduction",
help="external reduction factor",
type=float,
default=1.0)
parser.add_argument("--acquire",
help="mark points with acquire flag",
type=int,
default=1)
parser.add_argument("--groupRadius",
help="groupRadius in µm",
type=float,
default=7.0)
parser.add_argument(
"--numGroups",
help="number of groups for k-means groupOption",
type=int,
default=10,
)
parser.add_argument("--ptsPerGroup",
help="specify number of points per group",
type=int,
default=8)
parser.add_argument("--noBlurImage", help="", action="store_true")
parser.add_argument("--noBlurTemplate", help="", action="store_true")
args = parser.parse_args()
navfile = args.navfile
image = args.image
reduction = args.reduction
mapLabel = args.mapLabel
newLabel = args.newLabel
output = args.output
template = args.template
threshold = args.threshold
groupOption = args.groupOption
groupRadius = args.groupRadius
pixelSize = args.pixelSize
numGroups = args.numGroups
ptsPerGroup = args.ptsPerGroup
acquire = args.acquire
blurImage = not args.noBlurImage
blurTemplate = not args.noBlurTemplate
options = NavOptions(groupOption, groupRadius, pixelSize, numGroups,
ptsPerGroup, acquire)
param2 = args.param2
laceyThreshLow = args.laceyThreshLow
laceyThreshHigh = args.laceyThreshHigh
maxPts = args.maxPts
# clear output file to prevent merging previous points
createAutodoc(output, [])
# unnecessary options messages
if groupOption != 1:
if groupRadius is not None:
print(
"groupRadius will be ignored because groupOption is not 1 (groups by radius)"
)
if groupOption != 3 and numGroups is not None:
print(
"numGroups will be ignored because groupOption is not 3 (specify number of groups)"
)
if groupOption != 4 and ptsPerGroup is not None:
print(
"ptsPerGroup will be ignored because groupOption is not 4 (specify number of points per group)"
)
nav = openNavfile(navfile)
if mapLabel not in nav:
print("could not find map label: %s; aborting" % mapLabel)
exit()
elif not ("Regis" in nav[mapLabel] and "MapID" in nav[mapLabel]
and "StageXYZ" in nav[mapLabel]):
print(
"either Regis, MapID, and/or StageXYZ missing in section labeled %s; aborting"
% mapLabel)
exit()
# read and downsize images if necessary
image = imageio.imread(image)
if template is not None:
try:
template = imageio.imread(template)
template = imresize(template, 1 / (reduction))
except Exception as e:
print(e)
print("error reading in template %s; continuing without template" %
template)
template = None
if args.houghCircles == True:
print("using hough circles")
pts = houghCircles(image, pixelSize, param2=param2)
if maxPts is not None:
pts = getRandPts(pts, maxPts)
elif args.laceySearch == True:
if maxPts == None:
maxPts = 999
pts = laceySearch(image, maxPts, laceyThreshLow, laceyThreshHigh)
elif args.gui == True:
print("using template matching gui")
import semmatch.gui
pts, options = semmatch.gui.main(
image,
template,
threshold,
options,
blurImage=blurImage,
blurTemplate=blurTemplate,
)
if options.groupRadius is None:
print("invalid group radius; aborting")
exit()
if options.pixelSize is None:
print("invalid pixel size; aborting")
exit()
else:
print("using template matching non gui")
if template is None:
print("non-gui option must specify template")
exit()
pts = templateMatch(image,
template,
threshold,
blurImage=blurImage,
blurTemplate=blurTemplate)
# compensate round off error from reduction
pts = [Pt(x + 2, y) for x, y in pts]
pts = [Pt(int(reduction * x), int(reduction * y)) for x, y in pts]
if len(pts) == 0:
print("no matches found; exiting without creating %s" % output)
exit()
navPts = ptsToNavPts(pts, nav, mapLabel, newLabel, options)
createAutodoc(output, navPts)
print("%s created" % output)