{"action":"opened","issue":{"url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/3476","repository_url":"https://api.github.com/repos/CellProfiler/CellProfiler","labels_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/3476/labels{/name}","comments_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/3476/comments","events_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/3476/events","html_url":"https://github.com/CellProfiler/CellProfiler/issues/3476","id":293854172,"number":3476,"title":"NamesAndTypes error: ValueError: cannot reshape array of size 524288 into shape (512,512)","user":{"login":"burgerga","id":907362,"avatar_url":"https://avatars0.githubusercontent.com/u/907362?v=4","gravatar_id":"","url":"https://api.github.com/users/burgerga","html_url":"https://github.com/burgerga","followers_url":"https://api.github.com/users/burgerga/followers","following_url":"https://api.github.com/users/burgerga/following{/other_user}","gists_url":"https://api.github.com/users/burgerga/gists{/gist_id}","starred_url":"https://api.github.com/users/burgerga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/burgerga/subscriptions","organizations_url":"https://api.github.com/users/burgerga/orgs","repos_url":"https://api.github.com/users/burgerga/repos","events_url":"https://api.github.com/users/burgerga/events{/privacy}","received_events_url":"https://api.github.com/users/burgerga/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-02T11:14:12Z","updated_at":"2018-02-02T11:14:12Z","closed_at":null,"author_association":"NONE","body":"I am using Cellprofiler v2.2.1 installed via the conda method on Ubuntu 14.04 using the following conda environment: \r\n\r\n```\r\n# run: conda env create -f environment.yml\r\n# run: conda env update -f environment.yml\r\n# run: conda env remove -n cellprofiler\r\nname: cellprofiler2big\r\n# in order of priority: lowest (top) to highest (bottom)\r\nchannels:\r\n  - anaconda\r\n  - goodman # mysql-python for mac\r\n  - bioconda\r\n  - bjornfjohansson # wxpython 3.0.2.0\r\n  - conda-forge\r\n  - cyclus\r\ndependencies:\r\n  - appdirs\r\n  - cython\r\n  - h5py\r\n  - ipywidgets\r\n  - java-jdk\r\n  - jupyter\r\n  - libtiff\r\n  - libxml2\r\n  - libxslt\r\n  - lxml\r\n  - packaging\r\n  - pillow\r\n  - pip\r\n  - python=2\r\n  - pyzmq=15.3.0\r\n  - mahotas\r\n  - matplotlib!=2.1.0,>2.0.0\r\n  - mysql-python\r\n  - numpy\r\n  - raven\r\n  - requests\r\n  - scikit-image\r\n  - scikit-learn\r\n  - scipy\r\n  - sphinx\r\n  - tifffile\r\n  - wxpython=3.0.2.0\r\n  - pip:\r\n    - \"git+https://github.com/LeeKamentsky/python-javabridge.git@issue-121#egg=javabridge-issue-121\"\r\n    - cellh5\r\n    - centrosome\r\n    - inflect\r\n    - prokaryote==2.3.2\r\n    - python-bioformats==1.3.1\r\n    - \"git+https://github.com/CellProfiler/CellProfiler.git@v2.2.1#egg=cellprofiler-v2.2.1\"\r\n```\r\n\r\nWhen I run my pipeline I get the error: \r\n\r\n```\r\nValueError\r\nTraceback (most recent call last):\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/pipeline.py\", line 1956, in run_image_set\r\n    self.run_module(module, workspace)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/pipeline.py\", line 2067, in run_module\r\n    module.run(workspace)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/modules/namesandtypes.py\", line 1409, in run\r\n    stack)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/modules/namesandtypes.py\", line 1461, in add_image_provider\r\n    series, index, channel)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/modules/namesandtypes.py\", line 1494, in add_simple_image\r\n    cpmeas.IMAGE)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/modules/namesandtypes.py\", line 1513, in add_provider_measurements\r\n    img = m.get_image(name)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/measurements.py\", line 1616, in get_image\r\n    image = matching_providers[0].provide_image(self)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/modules/namesandtypes.py\", line 1988, in provide_image\r\n    image = LoadImagesImageProviderURL.provide_image(self, image_set)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/cellprofiler/modules/loadimages.py\", line 3230, in provide_image\r\n    channel_names=channel_names)\r\n  File \"/home/gerhard/miniconda2/envs/cellprofiler2big/lib/python2.7/site-packages/bioformats/formatreader.py\", line 816, in read\r\n    image.shape = (height, width)\r\nValueError: cannot reshape array of size 524288 into shape (512,512)\r\n```\r\n\r\nI get the same error on CellProfiler 3. Is this a dependency issue? I am willing to share images and pipeline if needed.\r\n\r\n(By the way, It would really help to get clearer Linux install instructions for both CellProfiler 3 and 2.2.1  (CP3 removed quite some functionality we use in our lab...))\r\n"}}
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