{"issue":{"created_at":"2011-11-23T20:39:19Z","state":"closed","updated_at":"2011-11-23T20:41:53Z","comments":0,"user":{"gravatar_id":"433a7fa3917a38691aa9914b61444875","id":473043,"url":"https://api.github.com/users/thouis","login":"thouis","avatar_url":"https://secure.gravatar.com/avatar/433a7fa3917a38691aa9914b61444875?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"body":"This issue was noticed when looking at this forum post:<a href=\"http://cellprofiler.org/forum/viewtopic.php?f=16&t=1463\">http://cellprofiler.org/forum/viewtopic.php?f=16&amp;t=1463</a><br/><br/>I have noticed the appearance of these files as well, even if I specify&quot;Do not write measurements&quot;. However, if an .h5 file must always be created, can it be cleaned up at the end if&quot;Do not write...&quot; is selected?<br/><br/>The forum poster is running headless, so I&#39;m not sure what recourse he has.<br/><br/>However, if I specify&quot;HDF5&quot; as the measurement format, and allow overwriting, I notice the following:<br/>(1) The output filename will be shown as&quot;DefaultOut.h5&quot; rather than the usual&quot;DefaultOUT.h5&quot; (note the case change)<br/>(2) Running the pipeline with the output filename in (1) will create a&quot;DefaultOUT&quot; file (no extension but it&#39;s an HDF5 file)<br/>(3) Changing the output filename to&quot;DefaultOUT.h5&quot; will create a DefaultOUT.h5 file on the run, as it should. But if I run it again, it get this error on the 1st image set:<br/>----------------------------------------------<br/>Traceback (most recent calllast):<br/>&nbsp;&nbsp;File&quot;C:\\Trunk\\CellProfiler\\cellprofiler\\gui\\pipelinecontroller.py&quot;, line 754,  in on_analyze_images<br/>&nbsp;&nbsp;&nbsp;&nbsp;m = cpm.Measurements(filename = output_path)<br/>&nbsp;&nbsp;File&quot;C:\\Trunk\\CellProfiler\\cellprofiler\\measurements.py&quot;, line 156, in __init__<br/>&nbsp;&nbsp;&nbsp;&nbsp;self.hdf5_dict = HDF5Dict(filename, is_temporary = is_temporary)<br/>&nbsp;&nbsp;File&quot;C:\\Trunk\\CellProfiler\\cellprofiler\\utilities\\hdf5_dict.py&quot;, line 115, in  __init__<br/>&nbsp;&nbsp;&nbsp;&nbsp;self.hdf5_file = h5py.File(self.filename,&#39;w&#39;)<br/>&nbsp;&nbsp;File&quot;C:\\Python27\\lib\\site-packages\\h5py\\_hl\\files.py&quot;, line 150, in __init__<br/>&nbsp;&nbsp;&nbsp;&nbsp;fid = make_fid(name, mode, fapl)<br/>&nbsp;&nbsp;File&quot;C:\\Python27\\lib\\site-packages\\h5py\\_hl\\files.py&quot;, line 51, in make_fid<br/>&nbsp;&nbsp;&nbsp;&nbsp;fid = h5f.create(name, h5f.ACC_TRUNC, fapl=plist)<br/>&nbsp;&nbsp;File&quot;h5f.pyx&quot;, line 89, in h5py.h5f.create (h5py\\h5f.c:1762)<br/>IOError: unable to create file (File accessability: Unable to open file)\n\nOriginal reporter: mbray\nJira link: https://jira.broadinstitute.org/browse/IMG-1531\nFix version: Current\nAssignee: leek\n\n**Comment from leek on Fri, 16 Sep 2011 11:49:21 -0400:**\nI answered the post. The files are needed to keep the measurements from<br/>consuming memory. They should be deleted at the end of the run.<br/><br/>On 9/16/2011 11:18 AM, Mark-Anthony Bray (JIRA) wrote:<br/>&gt; HDF5 file creation weirdness: File misnaming + locking<br/>&gt; ------------------------------------------------------<br/>&gt;<br/>&gt;                   Key:<a href=\"https://jira.broadinstitute.org/browse/IMG-1531\"title=\"HDF5 file creation weirdness: File misnaming + locking\">IMG-1531</a><br/>&gt;                   URL:<a href=\"https://jira.broadinstitute.org/browse/IMG-1531\">https://jira.broadinstitute.org/browse/IMG-1531</a><br/>&gt;               Project: Imaging<br/>&gt;            Issue Type: Bug<br/>&gt;            Components: CellProfiler<br/>&gt;      Affects Versions: Current<br/>&gt;              Reporter: Mark-Anthony Bray<br/>&gt;              Assignee: Lee Kamentsky<br/>&gt;              Priority: Major<br/>&gt;               Fix For: Current<br/>&gt;<br/>&gt;<br/>&gt; This issue was noticed when looking at this forum post:<a href=\"http://cellprofiler.org/forum/viewtopic.php?f=16&t=1463\">http://cellprofiler.org/forum/viewtopic.php?f=16&amp;t=1463</a><br/>&gt;<br/>&gt; I have noticed the appearance of these files as well, even if I specify&quot;Do not write measurements&quot;. However, if an .h5 file must always be created, can it be cleaned up at the end if&quot;Do not write...&quot; is selected?<br/>&gt;<br/>&gt; The forum poster is running headless, so I&#39;m not sure what recourse he has.<br/>&gt;<br/>&gt; However, if I specify&quot;HDF5&quot; as the measurement format, and allow overwriting, I notice the following:<br/>&gt; (1) The output filename will be shown as&quot;DefaultOut.h5&quot; rather than the usual&quot;DefaultOUT.h5&quot; (note the case change)<br/>&gt; (2) Running the pipeline with the output filename in (1) will create a&quot;DefaultOUT&quot; file (no extension but it&#39;s an HDF5 file)<br/>&gt; (3) Changing the output filename to&quot;DefaultOUT.h5&quot; will create a DefaultOUT.h5 file on the run, as it should. But if I run it again, it get this error on the 1st image set:<br/>&gt; ----------------------------------------------<br/>&gt; Traceback (most recent call last):<br/>&gt;    File&quot;C:\\Trunk\\CellProfiler\\cellprofiler\\gui\\pipelinecontroller.py&quot;, line 754,  in on_analyze_images<br/>&gt;      m = cpm.Measurements(filename = output_path)<br/>&gt;    File&quot;C:\\Trunk\\CellProfiler\\cellprofiler\\measurements.py&quot;, line 156, in __init__<br/>&gt;      self.hdf5_dict = HDF5Dict(filename, is_temporary = is_temporary)<br/>&gt;    File&quot;C:\\Trunk\\CellProfiler\\cellprofiler\\utilities\\hdf5_dict.py&quot;, line 115, in  __init__<br/>&gt;      self.hdf5_file = h5py.File(self.filename,&#39;w&#39;)<br/>&gt;    File&quot;C:\\Python27\\lib\\site-packages\\h5py\\_hl\\files.py&quot;, line 150, in __init__<br/>&gt;      fid = make_fid(name, mode, fapl)<br/>&gt;    File&quot;C:\\Python27\\lib\\site-packages\\h5py\\_hl\\files.py&quot;, line 51, in make_fid<br/>&gt;      fid = h5f.create(name, h5f.ACC_TRUNC, fapl=plist)<br/>&gt;    File&quot;h5f.pyx&quot;, line 89, in h5py.h5f.create (h5py\\h5f.c:1762)<br/>&gt; IOError: unable to create file (File accessability: Unable to open file)<br/>&gt;<br/>&gt; --<br/>&gt; This message is automatically generated by JIRA.<br/>&gt; For more information on JIRA, see:<a href=\"http://www.atlassian.com/software/jira\">http://www.atlassian.com/software/jira</a><br/><br/>\n\n","assignee":{"gravatar_id":"433a7fa3917a38691aa9914b61444875","id":473043,"url":"https://api.github.com/users/thouis","login":"thouis","avatar_url":"https://secure.gravatar.com/avatar/433a7fa3917a38691aa9914b61444875?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"id":2334304,"number":30,"pull_request":{"patch_url":null,"html_url":null,"diff_url":null},"labels":[{"name":"current","color":"e10c02","url":"https://api.github.com/repos/CellProfiler/CellProfiler/labels/current"}],"title":"JIRA [IMG-1531] HDF5 file creation weirdness: File misnaming + locking","closed_at":"2011-11-23T20:41:53Z","html_url":"https://github.com/CellProfiler/CellProfiler/issues/30","milestone":null,"url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/30"},"action":"closed"}