"iplane" data is missing in stat.npy files with manually selected ROIs (but exist in stat_orig.npy) #789
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carsen-stringer
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* add get_nd2_list method * remove comment * support pipelining nd2 files * support pipelining nd2 files * fix docstring and whitespaces * bug fix * final touch * Modified README to contain updated suite2p installation instructions for mac Ventura OS. Addresses issue MouseLand#897. * Fixed issue MouseLand#908 regarding badframes for register.py. 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Signed-off-by: dependabot[bot] <support@github.com> * Update issue templates * Update installation-issues.yml for issues * Rename installation-issues.yml to installation-issue.yml * Update installation issue.yml * Update bug_report.yml * Added bug_report.yml issue template * Update all issue templates * Update feature_request issue * Update feature_request.yml * Fixes issue MouseLand#914 for saving news ops parameters * Update documentation_issue.yml * Update documentation_issue.yml * Fixes multiplane issue MouseLand#905 with save_nwb * Fixes issue MouseLand#904 for 2 channel manual labeling * Update .readthedocs.yml * remove spaces * conform to function signature and usage pattern a few lines above * add nd2 in requirements * minor revision * new logic * refactor dim sorting * revert to previous code * Fixes the from_stat_dict bug mentioned in MouseLand#935. * Update run suite2p jupyter notebook to fix issue MouseLand#935 * Addresses MouseLand#930 in which bin_data has trouble dealing with cases in which the current batch has fewer frames than the bin_size * removed ops assignment * removed deprecated np.bool * Update the version of the dependencies for suite2p * Update np.bool to 'bool' to account for numpy deprecation with latest version * Add Sparse detection to gui as a setting for running suite2p * Addresses MouseLand#951 and adds nd2 as an input to gui * Fix issue with np.asanyarray being changed in numpy 1.24.4 * addressed IndexError * Update README.md * Update README.md * fixing skip torch if version 2.0 * adding pep8 style to repo * fixing dictionary splitting * modifying imports * converting to "" from '' * converting binaryfile to memmap * rewriting binarycombined * removing scanimage-tiff-reader for now * fixing dragging in gui and linewidth=88 * removing old testing yml * adding py39, updating readme * adding option for MouseLand#955 * fixing bug in docstring (MouseLand#902) * adding iplane to saved manual ROIs (MouseLand#789) * fixing MouseLand#747 saving to mat * making nd2 and scanimage-tiff-reader optional (MouseLand#950) * removing bruker dependency on scanimage-tiff-reader * Create codecov.yml * Update README.md * Update README.md * Update README.md * Update README.md * Update BinaryRWFile name usage to BinaryFile * Add instructions on how to use test_data generation script * Added instructions on generating new test data * Add method for writing tiff for binaryFile class * Update write_tiff for binary.py to crop frames, x, and y too * fix frame range issue with write_Tiff for binary * added debugging logs * removed debugging logs * removed print statement * removed unnecessary space * Fixes MouseLand#943 to address documentation issue with high_pass * adding copyright to every py file * Delete .dvc directory * fixing import error with h5py and paramiko MouseLand#987 * Update README.md * Add pynwb package to setup.py as tests needs pynwb for one of the io_tests * Update readme.md to be for python version 3.9 * Addresses MouseLand#944 leading zero issue with tiff filename. * Addresses MouseLand#944 leading zero issue with tiff filename. * Update save_path0 to close MouseLand#991. * Update save_path0 to close MouseLand#991. * update visualize.py to import rastermap properly * Re-add connected to GUI options * Update README.md Remove note about scanimage-tiff-reader mac incompatibility * Update README.md Simplify mac os instructions * Update setup.py Update rastermap requirement based on issue ticket suggestions * Update setup.py * Updated jupyter notebook to work with new binaryFile class in suite2p.io * Updated jupyter notebook name * Update colab 2023 to fully fix MouseLand#1011 and update some comments on notebook * Updated jupyter notebook to work with new binaryFile class in suite2p.io * Updated jupyter notebook name * Update colab 2023 to fully fix MouseLand#1011 and update some comments on notebook * adding pyqt6 and switching to qtpy * updating readme and fixing spelling error in copyright * adding license notice * adding check in setup.py for installation of a pyqt version * adding tutorial * Update tutorial.md with additional comments * Update suite2p gui to work with QFileDialog.Options() not working with pyqt6 * Update binary.py write_tiff to add all frames to a single series * Updated tiff.py to use contiguous parameter * Update README.md * checking h5py key to open binaries before data_path * fixing bug in code * adding new data type * adding support for binary and mp4/avi files * enabling ops.json loading in reggui and binary-only processing * increase tolerance on classification regression test * add more tolerance * increasing tolerance again * increasing tolerance again * Update README.md * Add explanation for how to apply classifiers * CheckState Fix * Fix conda environment creation for developers * Update utils.py * Update README.md to fix MouseLand#1060. Updates badge links for tests and docs * Update merge.py of gui subpackage to not use deprecated np.bool * Update merge.py of gui subpackage to not use deprecated np.bool * Add import to gui/io.py * Update gui.rst to have clearer instructions for MouseLand#1002. * bug in h5py key option * adding support for multipage bruker ome tiffs * Update inputs.rst to include multipage bruker instructions * Update inputs.rst * Added support for Thorlabs RAW files (io.raw) * Added xmltodict * Update raw.py- todo verified * safe import for xmltodict * fixing bug with multiplane registration * allowing reg_file input to compute_zpos * fixing bug with multi-plane nonrigid ops * add support for Hamamatsu DCIMG format * add support for Hamamatsu DCIMG format * add dcimg_deps to all_deps and restrict cellpose to <3.0 * Addresses MouseLand#1093 with cellpose method having too many arguments * Addresses MouseLand#1093 with cellpose method having too many arguments * remove cellpose<3.0 restriction * Fixes issue MouseLand#1101 with older version of cellpose * Update zalign.py Made sure that if a reg_file is given to the zalign function it uses it, rather than the ops reg_file * Update setup.py * adding dcimg * removing dcimg extra --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: tdincer <tolgadincer@gmail.com> Co-authored-by: Chris Ki <chriski777@berkeley.edu> Co-authored-by: Chris Ki <cski@andrew.cmu.edu> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: carsen-stringer <carsen.stringer@gmail.com> Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com> Co-authored-by: itsb <itsb@users.noreply.github.com> Co-authored-by: Sidharth Hulyalkar <sid.soccer.21@gmail.com> Co-authored-by: Ahmed Morsi <amorsi@berkeley.edu> Co-authored-by: Marius Pachitariu <marius10p@gmail.com> Co-authored-by: Heather Ratigan <hmacomber@uchicago.edu> Co-authored-by: Ryan Ly <rly@lbl.gov> Co-authored-by: Arielle Leon <ariellel@alleninstitute.org> Co-authored-by: Andrew Landau <andrewtylerlandau@gmail.com> Co-authored-by: arielleleon <54869022+arielleleon@users.noreply.github.com> Co-authored-by: yaelpri <yael.prilutski@gmail.com> Co-authored-by: yaelpri <61921608+yaelpri@users.noreply.github.com> Co-authored-by: Yael Prilutski <61921608+yael-prilutski@users.noreply.github.com> Co-authored-by: nguyemi5 <nguyemi5@github.com> Co-authored-by: nguyemi5 <38402644+nguyemi5@users.noreply.github.com> Co-authored-by: liadJB <48135253+liadJB@users.noreply.github.com>
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Hi,
I need to select all ROIs manually because the expression is very sparse and my image is noisy.. After extracting ROIs, I want to drop one of the planes, but "iplane" data is missing in stat.npy files. When I try it on original data, it works. does anyone have a suggestion about how I could drop plane in processed stat files as well?
Thanks in advance!
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