- #CELLPROFILER YOU MUST SPECIFY A PIPELINE FILENAME TO RUN MAC OS X#
- #CELLPROFILER YOU MUST SPECIFY A PIPELINE FILENAME TO RUN INSTALL#
- #CELLPROFILER YOU MUST SPECIFY A PIPELINE FILENAME TO RUN CODE#
Mon Apr 13 00:12:15 2020: Image # 1, module Groups # 4: 0.00 secĮrror detected during run of module MeasureImageAreaOccupiedįile “/home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/pipeline.py”, line 1763, in run_with_yieldįile “/home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/pipeline.py”, line 2007, in run_moduleįile “/home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/modules/measureimageareaoccupied.py”, line 281, in run Times reported are CPU times for each module, not wall-clock time
#CELLPROFILER YOU MUST SPECIFY A PIPELINE FILENAME TO RUN CODE#
home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/importlib/ init.py:37: H5pyDeprecationWarning: The h5py.highlevel module is deprecated, code should import directly from h5py, e.g. Hdf5_type_is_float = np.issubdtype(hdf5_type, float) In future, it will be treated as np.float64 = np.dtype(float).type. home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/utilities/hdf5_dict.py:529: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.int64 = np.dtype(int).type. home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/utilities/hdf5_dict.py:527: FutureWarning: Conversion of the second argument of issubdtype from int to np.signedinteger is deprecated. ImportError: this is MySQLdb version (1, 2, 5, ‘final’, 1), but _mysql is version (1, 4, 6, ‘final’, 0)
#CELLPROFILER YOU MUST SPECIFY A PIPELINE FILENAME TO RUN INSTALL#
Can you please advise what I am doing wrong? I already have run ‘sudo apt install python-mysqldb’ and the package exists already.Ĭellprofiler -p mask_measurement.cppipe -c -r -i -o įile “/home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/modules/exporttodatabase.py”, line 87, inįile “/home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/MySQLdb/ init.py”, line 23, in My pipeline file as well a sample folder of masks is attached. I exported the cppipe file to my Ubuntu machine and ran cellprofiler (v3.0.0rc3) from the command line as follows and run into the error below.
#CELLPROFILER YOU MUST SPECIFY A PIPELINE FILENAME TO RUN MAC OS X#
The Analyze Images works great on my Mac OS X Mojave with Cellprofiler 3.0.0. I am attaching a simple pipeline file I created to measure object sizes of a bunch of binary masks. –> 905 klass = env.find_class(class_name)ĩ07 jexception = get_env().exception_occurred()ĪttributeError: ‘NoneType’ object has no attribute ‘find_class’īackports.shutil-get-terminal-size=1.0.0 home/jagadish/.local/lib/python2.7/site-packages/javabridge/jutil.pyc in make_static_call(class_name, method_name, sig) –> 934 fn = make_static_call(class_name, method_name, sig)ĩ35 args_sig = split_sig(sig) home/jagadish/.local/lib/python2.7/site-packages/javabridge/jutil.pyc in static_call(class_name, method_name, sig, *args) home/jagadish/.local/lib/python2.7/site-packages/javabridge/jutil.pyc in class_for_name(classname, ldr)ġ738 ldr = static_call(‘java/lang/ClassLoader’, ‘getSystemClassLoader’,ġ740 return static_call(‘java/lang/Class’, ‘forName’,ġ741 ‘(Ljava/lang/String ZLjava/lang/ClassLoader )’ –> 324 ifcls = J.class_for_name(“”)ģ25 scls = env.find_class(“java/lang/String”) home/jagadish/yeast_web/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/cellprofiler/modules/images.pyc in prepare_run(self, workspace) In run_pipeline(pipeline_filename, image_dict) > 1 workspace = run_pipeline(pipeline_filename, images) I am using the sample notebook cellprofiler_demo.ipynb at and modifying it to run my pipeline.ĪttributeError Traceback (most recent call last) What am I doing wrong? Any help will be appreciated.
Whenever I try to run the pipeline which ran fine on my Mac OS, I get the following error. The pip freeze and java versions are given below. I then exported the pipeline file and copied it over to a Conda environment on a Ubuntu machine that has cellprofiler installed. It runs fine on a sample set of images and produces the desired output. I created a pipeline using the CellProfiler 3.0.0 app on my Mac OS X.
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