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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Andy,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I think that you should try to include the full name of the file between square brackets. I didn’t try for this specific command, but this is the common practice
when file names contain spaces (otherwise the script interpreter reads only the substring before the space).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">run(“Bio-Formats”, “open=[/path/to my/file]”);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I hope it helps,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Giovanni<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>Clark Andrew<br>
<b>Sent:</b> Dienstag, 12. Februar 2019 13:02<br>
<b>To:</b> ome-users@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> [ome-users] FIJI bio-formats importer cannot open paths with spaces (from macro)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">There’s a small issue with calling the bio-formats importer from a FIJI macro. It will not open a file if there is a space anywhere in the file path. For example:
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">run(“Bio-Formats”, “open=/path/to my/file”);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">will raise the following error:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The specified file (/path/to) does not exist.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I tried replacing the spaces with “\ “ or putting the filepath in double quotes, but I get the same error.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This is on a freshly updated FIJI and bio-formats on OSX. There is no problem opening the file using the Bio-Formats importer from the dropdown plugins menu, only running it from a macro script.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks!<o:p></o:p></p>
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<p class="MsoNormal">andy <o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">____________________<br>
Andrew G. CLARK, PhD<br>
Postdoctoral Fellow<br>
VIGNJEVIC Group<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><br>
+33 (0) 156 24 67 70<br>
<a href="mailto:andrew.clark@curie.fr">andrew.clark@curie.fr</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><a href="http://www.andrewgclark.info">www.andrewgclark.info</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Institut Curie / UMR 144<br>
12, Rue Lhomond<br>
75005 Paris<br>
FRANCE<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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