i dont understand how can i use the run method of the ij.plugin ImageCalculator Class to return a ImagePlus object instead of void. I tested the script from here: https://imagej.nih.gov/ij/developer/api/ij/ij/plugin/ImageCalculator.html in my python script and got: AttributeError: 'NoneType' object has no attribute 'show'.
My script:
import os
from ij import WindowManager, IJ
from ij.plugin import ImageCalculator as ic
dir = "path to my files"
imp1 = WindowManager.getImage(dir + "bgn0.tif")
for file in os.listdir(dir):
filename = file
if filename.endswith(".tif"):
imp2 = WindowManager.getImage(filename)
imp3 = ic().run("subtract create", imp1, imp2);
imp3.show();
IJ.saveAsTiff(imp3, dir + "\subtracted\\" + filename)
I aim for using this script with ImageJ to use background subtraction on all files in a target folder. Finally i want to save the images in the "subtracted" sub folder.
Related
By default Yocto adds build timestamp to the output image file name, but I would like to replace it by the revision of my integration Git repository (which references all my layers and configuration files). To achieve this, I put the following code to my image recipe:
def get_image_version(d):
import subprocess
import os.path
try:
parentRepo = os.path.dirname(d.getVar("COREBASE", True))
return subprocess.check_output(["git", "describe", "--tags", "--long", "--dirty"], cwd = parentRepo, stderr = subprocess.DEVNULL).strip().decode('UTF-8')
except:
return d.getVar("MACHINE", True) + "-" + d.getVar("DATETIME", True)
IMAGE_VERSION = "${#get_image_version(d)}"
IMAGE_NAME = "${IMAGE_BASENAME}-${IMAGE_VERSION}"
IMAGE_NAME[vardepsexclude] = "IMAGE_VERSION"
This code works properly until I change Git revision (e.g. by adding a new commit). Then I receive the following error:
ERROR: When reparsing /home/ubuntu/yocto/poky/../mylayer/recipes-custom/images/core-image-minimal.bb.do_image_tar, the basehash value changed from 63e1e69797d2813a4c36297517478a28 to 9788d4bf2950a23d0f758e4508b0a894. The metadata is not deterministic and this needs to be fixed.
I understand this happens because the image recipe has already been parsed with older Git revision, but why constant changes of the build timestamp do not cause the same error? How can I fix my code to overcome this problem?
The timestamp does not have this effect since its added to vardepsexclude:
https://docs.yoctoproject.org/bitbake/bitbake-user-manual/bitbake-user-manual-metadata.html#variable-flags
[vardepsexclude]: Specifies a space-separated list of variables that should be excluded from a variable’s dependencies for the purposes of calculating its signature.
You may need to add this in a couple of places, e.g.:
https://git.yoctoproject.org/poky/tree/meta/classes/image-artifact-names.bbclass#n7
IMAGE_VERSION_SUFFIX ?= "-${DATETIME}"
IMAGE_VERSION_SUFFIX[vardepsexclude] += "DATETIME SOURCE_DATE_EPOCH"
IMAGE_NAME ?= "${IMAGE_BASENAME}-${MACHINE}${IMAGE_VERSION_SUFFIX}"
After some research it turned out the problem was in this line
IMAGE_VERSION = "${#get_image_version(d)}"
because the function get_image_version() was called during parsing. I took inspiration from the source file in aehs29's post and moved the code to the anonymous Python function which is called after parsing.
I also had to add vardepsexclude attribute to the IMAGE_NAME variable. I tried to add vardepvalue flag to IMAGE_VERSION variable as well and in this particular case it did the same job as vardepsexclude. Mentioned Bitbake class uses both flags, but I think in my case using only one of them is enough.
The final code is below:
IMAGE_VERSION ?= "${MACHINE}-${DATETIME}"
IMAGE_NAME = "${IMAGE_BASENAME}-${IMAGE_VERSION}"
IMAGE_NAME[vardepsexclude] += "IMAGE_VERSION"
python () {
import subprocess
import os.path
try:
parentRepo = os.path.dirname(d.getVar("COREBASE", True))
version = subprocess.check_output(["git", "describe", "--tags", "--long", "--dirty"], cwd = parentRepo, stderr = subprocess.DEVNULL).strip().decode('UTF-8')
d.setVar("IMAGE_VERSION", version)
except:
bb.warning("Could not get Git revision, image will have default name.")
}
EDIT:
After some research I realized it's better to define a global variable in layer.conf file of the layer containing the recipes referencing the variable. The variable is set by a python script and is immediately expanded to prevent deterministic build warning:
layer.conf:
require conf/image-version.py.inc
IMAGE_VERSION := "${#get_image_version(d)}"
image-version.py.inc:
def get_image_version(d):
import subprocess
import os.path
try:
parentRepo = os.path.dirname(d.getVar("COREBASE", True))
return subprocess.check_output(["git", "describe", "--tags", "--long", "--dirty"], cwd = parentRepo, stderr = subprocess.DEVNULL).strip().decode('UTF-8')
except:
bb.warn("Could not determine image version. Default naming schema will be used.")
return d.getVar("MACHINE", True) + "-" + d.getVar("DATETIME", True)
I think this is cleaner approach which fits BitBake build system better.
I have a class that I want to share between different files or computers? I can pickle and load it from the same jupyter notebook. However, I cannot load it from a different machine/or different notebook. I have tried the following,
Initialize and and save from a jupyter notebook
# Simplified class definition
class MyClass:
def __init__(self, name):
self.name = name
self.dataToIndex = {}
self.index = 0
def addData(self, dataReceived):
self.dataToIndex[dataReceived] = self.index
self.index += 1
# initialize
my_dataset = MyClass("My_test_dataset")
# add some data
my_dataset.addData("One")
my_dataset.addData("Two")
# check data
my_dataset.dataToIndex
# save from one juputer notebook
import pickle
with open("path.obj", "wb") as inp:
pickle.dump(my_dataset, inp, pickle.HIGHEST_PROTOCOL)
# Read from the same jupyter notebook
with open("path.obj", 'rb') as inp:
transferred = pickle.load(inp)
# Output looks good
transferred.dataToIndex
{'One': 0, 'Two': 1}
Read from the new jupyter notebook
import pickle
with open("path.obj", 'rb') as inp:
transferred = pickle.load(inp)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-1-44a1a18ebb1b> in <module>
2 # Read from the same jupyter notebook
3 with open("path.obj", 'rb') as inp:
----> 4 transferred = pickle.load(inp)
AttributeError: Can't get attribute 'MyClass' on <module '__main__'>
Now, I want to be able to load into a different python script on in a different jupyter notebook.
I have checked this, Saving an Object (Data persistence)
and
https://www.stefaanlippens.net/python-pickling-and-dealing-with-attributeerror-module-object-has-no-attribute-thing.html
But could not figure out a solution. Any help is appreciated.
There is a tons of helpful posts on this. However, most of those fall under, how to save from within the class etc. For a future beginner like me, I just want to provide a simple solution that worked for me.
Take the class out of the notebook and put in a script like, my_class_def.py
class MyClass:
def __init__(self, name):
self.name = name
self.dataToIndex = {}
self.index = 0
def addData(self, dataReceived):
self.dataToIndex[dataReceived] = self.index
self.index += 1
Then use the pickle to save as it is.
In the different(new) script, import the class first using,
from my_class_def import MyClass
and then load the picked file.
Could you anyone please findout the rootcause of the below error
import org.apache.poi.ss.usermodel.*;
import org.apache.poi.hssf.usermodel.*;
import org.apache.poi.xssf.usermodel.*;
import org.apache.poi.ss.util.*;
import org.apache.poi.ss.usermodel.*;
import java.io.*;
//def groovyUtils = new com.eviware.soapui.support.GroovyUtils(context)
File file=new File("C://Users/toothless/Desktop/Don Delete/MyPractice.xlsx")
Workbook workbook = Workbook.getWorkbook(file)
Sheet sheet=workbook.getSheet(0)
rc=sheet.getRows()
log.info rc
Following is my ext folder screenshot.
I'm getting the following error while executing the above groovy code.
groovy.lang.MissingMethodException: No signature of method: static org.apache.poi.ss.usermodel.Workbook.getWorkbook() is applicable for argument types: (java.io.File) values: [C:\Users\toothless\Desktop\Don Delete\MyPractice.xlsx] error at line: 10
First there is no method like you mention Workbook.getWorkbook. Ref doc. Here your question to read excel file as workbook object use the code shown below,
For xlsx files :
XSSFWorkbook wb = new XSSFWorkbook (file)
For xls files :
HSSFWorkbook wb = new HSSFWorkbook (file)
After that you can use these methods shown in doc for further reading process.
I am trying to create test runner python file, that executes the pytest.exe in particular testcase folder and send the results via email.
Here is my code:
test_runner.py:
try:
command = "pytest.exe {app} > {log}".format(app=app_folder, log = log_name)
os.system(command)
except:
send_mail()
I use the following code in conftest.py to add screenshots to pytest-html report.
In conftest.py:
#pytest.mark.hookwrapper
def pytest_runtest_makereport(item, call):
pytest_html = item.config.pluginmanager.getplugin('html')
outcome = yield
report = outcome.get_result()
extra = getattr(report, 'extra', [])
if pytest_html:
xfail = hasattr(report, 'wasxfail')
if (report.skipped and xfail) or (report.failed and not xfail):
test_case = str(item._testcase).strip(")")
function_name = test_case.split(" ")[0]
file_and_class_name = ((test_case.split(" ")[1]).split("."))[-2:]
file_name = ".".join(file_and_class_name) + "." + function_name
Issue is, when I run the command "pytest.exe app_folder" in windows command prompt it is able to discover the test cases and execute them and get the results. But when I call the command from .py file either using os.command or subprocess it fails with the following exception:
\conftest.py", line 85, in pytest_runtest_makereport
INTERNALERROR> test_case = str(item._testcase).strip(")")
INTERNALERROR> AttributeError: 'TestCaseFunction' object has no attribute
'_testcase'
Can anyone please help me to understand whats happening here? or any other way to get the testcase name?
Update:
To overcome this issue, I alternatively used the TestResult object from pytest_runtest_makereport hook to get the test case details.
#pytest.mark.hookwrapper
def pytest_runtest_makereport(item, call):
outcome = yield
report = outcome.get_result()
In the above example, report variable contain the TestResult object. This can be manipulated to get the testcase/class/module name.
you can use shell=True option with subprocess to get the desired result
from subprocess import Popen
command='pytest.exe app_folder' #you can paste whole command which you run in cmd
p1=Popen(command,shell=True)
This would solve your purpose
I'm using Python 2.6.6 and pyglet 1.1.4. In my "Erosion" folder, I have "Erosion.py" and a folder named "Images." Inside images, there are .png images. One image is named "Guard.png."
In "Erosion.py" there is a segment that goes like so:
pyglet.resource.path = ['Images']
pyglet.resource.reindex()
self.image = pyglet.resource.image('%s%s' % (character, '.png'))
When I run this, I am given
File "C:\Python26\lib\site-packages\pyglet\resource.py", line 394, in file raise ResourceNotFoundException(name)
ResourceNotFoundException: Resource "Guard.png" was not found on the path. Ensure that the filename has the correct captialisation.
I have tried changing the path to ['./Images'] and ['../Images']. I've also tried removing the path and the reindex call and putting Erosion.py and Guard.png in the same folder.
This is what i do to be able to load resources:
pyglet.resource.path = ['C:\\Users\\myname\\Downloads\\temp']
pyglet.resource.reindex()
pic = pyglet.resource.image('1.jpg')
texture = pic.get_texture()
gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MAG_FILTER, gl.GL_NEAREST)
texture.width = 960
texture.height = 720
texture.blit(0, 0, 0)
try this
pyglet.image.load('path/to/image.png')
If the relative path is not working you can try with the absolute path using the os module.
import pyglet
import os
working_dir = os.path.dirname(os.path.realpath(__file__))
pyglet.resource.path = [os.path.join(working_dir,'Images')]
pyglet.resource.reindex()
image = pyglet.resource.image('character.png'))
It's better to use the os.path.join method instead of writing it as a string for a better cross-platform support.
I get a problem like this using pyglet and pyscripter.(the text editor) In order for the file to be found I have to restart the editor before running the program.
This might be a problem with pyscripter however.
It is worth looking into: http://pyglet.readthedocs.io/en/pyglet-1.3-maintenance/programming_guide/resources.html
You should include all the directories into:
pyglet.resource.path = [...]
Then pass the ONLY the file name when you call:
pyglet.resource.image("ball_color.jpeg")
Try:
import os
import pyglet
working_dir = os.path.dirname(os.path.realpath(__file__))
image_dir = os.path.join(working_dir, 'images')
sound_dir = os.path.join(working_dir, 'sound')
print working_dir
print "Images are in: " + image_dir
print "Sounds are in: " + sound_dir
pyglet.resource.path = [working_dir, image_dir, sound_dir]
pyglet.resource.reindex()
try:
window = pyglet.window.Window()
image = pyglet.resource.image("ball_color.jpeg")
#window.event
def on_draw():
window.clear()
image.blit(0, 0)
pyglet.app.run()
finally:
window.close()
The use of try and finally are not necessary, but they are recommended. You might end up with a lot of open windows and pyglet back processes if you don't close the window when there are errors.
pyglet 1.4.4 format: HUD_img = pyglet.resource.image('ui\ui_gray_block_filled.png')
pyglet 1.4.8 format: HUD_img = pyglet.resource.image('ui/ui_gray_block_filled.png')
I was using pyglet 1.4.4 and was able to use this the first format.
After upgrading to pyglet 1.4.8 I had the error: pyglet.resource.ResourceNotFoundException: Resource "your_resource_path" was not found on the path.
Switching to the 2nd format with forward slashes solved this issue for me. Not sure why this change was made...I'm sure there was a good reason for it.