No such file or dir: u'/ - /CpmeasurementXXXXXX.hdf5'


#1

Hi Everyone,

I’m getting hit with a possible bug. My pipeline worked until I added a measure size shape; now I get

Exception in thread AnalysisRunner.interface:
Traceback (most recent call last):
File “threading.py”, line 801, in __bootstrap_inner
File “threading.py”, line 754, in run
File “cellprofiler/analysis.py”, line 439, in interface
File “cellprofiler/measurement.py”, line 1807, in load_measurements_from_buffer
File “cellprofiler/measurement.py”, line 1838, in load_measurements
IOError: [Errno 2] No such file or directory: u’//Cpmeasurementsk4o6FX.hdf5’

I’ve not selected hdf5 output but maybe this is just caching the measurements as it goes? I’ve tried to create this but I guess the last 6 characters are being generated. How can I fix?

J


#2

After ‘complete’ removal I’m getting the below right after I click Analyze. My pipeline has no measurement modules whatsoever. :frowning:

Starting workers on address tcp://127.0.0.1:50668
Progress Counter({u’Unprocessed’: 1800})
Worker 0: [15836] PyInstaller Bootloader 3.x
Worker 0: [15836] LOADER: executable is /Applications/CellProfiler-3.0.0.app/Contents/MacOS/cp
Worker 0: [15836] LOADER: homepath is /Applications/CellProfiler-3.0.0.app/Contents/MacOS
Worker 0: [15836] LOADER: _MEIPASS2 is NULL
Worker 0: [15836] LOADER: archivename is /Applications/CellProfiler-3.0.0.app/Contents/MacOS/cp
Worker 0: [15836] LOADER: /Applications/CellProfiler-3.0.0.app/Contents/MacOS/cp contains a digital signature
Worker 0: [15836] LOADER: No need to extract files to run; setting extractionpath to homepath
Worker 0: [15836] LOADER: Already in the child - running user’s code.
Worker 0: [15836] LOADER: Python library: /Applications/CellProfiler-3.0.0.app/Contents/MacOS/Python
Worker 0: [15836] LOADER: Loaded functions from Python library.
Worker 0: [15836] LOADER: Manipulating environment (sys.path, sys.prefix)
Worker 0: [15836] LOADER: sys.prefix is /Applications/CellProfiler-3.0.0.app/Contents/MacOS
Worker 0: [15836] LOADER: Setting runtime options
Worker 0: [15836] LOADER: Initializing python
Worker 0: [15836] LOADER: Overriding Python’s sys.path
Worker 0: [15836] LOADER: Post-init sys.path is /Applications/CellProfiler-3.0.0.app/Contents/MacOS
Worker 0: [15836] LOADER: Setting sys.argv
Worker 0: [15836] LOADER: setting sys._MEIPASS
Worker 0: [15836] LOADER: importing modules from CArchive
Worker 0: [15836] LOADER: extracted struct
Worker 0: [15836] LOADER: callfunction returned…
Worker 0: [15836] LOADER: extracted pyimod01_os_path
Worker 0: [15836] LOADER: callfunction returned…
Worker 0: [15836] LOADER: extracted pyimod02_archive
Worker 0: [15836] LOADER: callfunction returned…
Worker 0: [15836] LOADER: extracted pyimod03_importers
Worker 0: [15836] LOADER: callfunction returned…
Worker 0: [15836] LOADER: Installing PYZ archive with Python modules.
Worker 0: [15836] LOADER: PYZ archive: out00-PYZ.pyz
Worker 0: [15836] LOADER: Running pyiboot01_bootstrap.py
Worker 0: [15836] LOADER: Running pyi_rth_traitlets.py
Worker 0: [15836] LOADER: Running pyi_rth_mplconfig.py
Worker 0: [15836] LOADER: Running pyi_rth_mpldata.py
Worker 0: [15836] LOADER: Running pyi_rth_pkgres.py
Worker 0: [15836] LOADER: Running pyi_rth_multiprocessing.py
Worker 0: [15836] LOADER: Running CellProfiler.py
Worker 0: Starting job
Progress Counter({u’Unprocessed’: 1799, u’InProcess’: 1})
Worker 0: Error in worker
Worker 0: Traceback (most recent call last):
Worker 0: File “cellprofiler/worker.py”, line 357, in do_job
Worker 0: File “cellprofiler/measurement.py”, line 1807, in load_measurements_from_buffer
Worker 0: File “cellprofiler/measurement.py”, line 1838, in load_measurements
Worker 0: IOError: [Errno 2] No such file or directory: u’/Volumes/Files/moldev-imxpress/23754-Out/Cpmeasurementswl4p22.hdf5’
Worker 0: Cancelling worker


#3

I use jenv to manipulate my Java vars. Currently this is running on 1.8u181 (which I think is supported).


#4

Hmm, if it were a Java issue I’d expect CP wouldn’t load at all. Just to confirm, CP has write permissions in that output folder? Can you give us your CP version and a pip freeze? Thanks!