Check the module(s) in CellProfiler that you know use a similar type of setting, and see how it is implemented there.Ĭ -> "Yes" Settings that have just moved to core, but are not part of a larger section.Search the core repository for your setting name.If you find your setting is not represented here, you have a couple of options. We provide here a non-comprehensive list of setting updates. The setting library underwent perhaps the biggest outward-facing change in the 3->4 migration. If you find yourself running into the error NameError: name 'cellprofiler' is not defined, the line in question throwing it may have a functionality that moved to core.Īt minimum, you will commonly need to upgrade the following importsĬellprofiler.image -> cellprofiler_core.imageĬasurement -> cellprofiler_asurementĬellprofiler.module -> cellprofiler_core.moduleĬellprofiler.object -> cellprofiler_core.objectĬellprofiler.pipeline -> cellprofiler_core.pipelineĬtting -> cellprofiler_ttingĬellprofiler.workspace -> cellprofiler_core.workspace Many of CellProfiler's backbone functionality - things like the workspace, the settings, the pipelines, etc have moved to a new package called cellprofiler_core. Many tools and guides online have been written to guide developers in making these changes- we cannot reproduce them all here, but we find this guide helpful, and welcome others' experience in making these upgrades. If you work to finish updating a plugin from 3.X to 4.X, we encourage you to contribute your updated version back here to the repository, and/or to add to this guide to help others migrate modules more easily! Python2 to Python3Īny aspects of your code that use Python2 syntax will not work, as CellProfiler 4 is written in Python3. Our team may complete the upgrade of plugins from CellProfiler3.X to 4.X from time to time as we have time and/or need them, but we do not guarantee maintenance of modules here in the plugins repository - that is the ultimate responsibility of the author. Note that these have not been verified to be completely migrated, nor to run- only plugins in the top folder of the repository should be considered fully CellProfiler4-compatible. The CellProfiler team has performed a preliminary migration of CellProfiler3 plugins to CellProfiler4- these may be found in the CellProfiler4_AutoConvert folder. (This guide is currently under construction)ĬellProfiler 4.0 is our first Python3 release and has a number of under-the-hood changes, which means upgrading CellProfiler 3 pipelines to CellProfiler 4 will require some updates to your plugins to work nicely in the new systems.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |