{"push_id":1912287037,"size":14,"distinct_size":1,"ref":"refs/heads/use_lsf","head":"6df5619eaa6e3acd5b2583b664e784ff7eb3f925","before":"1c8e3929d49599c088af542838fe01b123b3866a","commits":[{"sha":"f528f4933358e691286365b5104062ee8b840ce4","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Drop initial rechunk in registration\n\nInstead of calling `rechunk` right after loading data for image\nregistration, simply set the desired chunking when loading the data in\nthe first place. This way the additional `rechunk` call at the beginning\nof the image registration can be dropped entirely.","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/f528f4933358e691286365b5104062ee8b840ce4"},{"sha":"f9d3582fd6516697c1106d26669ab589e9f390f6","author":{"name":"jakirkham","email":"a65f82840b865057a74adf67d85c39540fb3eecd@gmail.com"},"message":"Merge pull request #97 from jakirkham/drop_reg_rechunk\n\nDrop initial rechunk in registration","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/f9d3582fd6516697c1106d26669ab589e9f390f6"},{"sha":"818d8232d67204437a386106c7cd92e39bdd6855","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Use Real FFTs in Denoising\n\nAs the input to denoising is real and all operations applied in\nthe denoising step are real, we should be able to just use real FFTs to\ntransform the data into and out of frequency space. Hence these changes\nmake use of real FFTs to transform the data before filtering and then\nuse real FFTs to invert the filtered data and get back the result.","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/818d8232d67204437a386106c7cd92e39bdd6855"},{"sha":"64530bfac53eb6e5e38b95fcf91e1d092e7b83c1","author":{"name":"jakirkham","email":"a65f82840b865057a74adf67d85c39540fb3eecd@gmail.com"},"message":"Merge pull request #98 from jakirkham/denoise_rfft\n\nUse Real FFTs in Denoising","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/64530bfac53eb6e5e38b95fcf91e1d092e7b83c1"},{"sha":"1d3334aeec62a2797b2f89ba896a1e1d7b165759","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Use Real FFTs in Image Registration\n\nIn order to speed up image registration a bit, make use of Real FFTs\nboth to convert individual frames to frequency space and to find the\nconvolution of frames with the template image in real space. Given the\nimages and the result of the convolution should be real, these are\nreasonable constraints to make.","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/1d3334aeec62a2797b2f89ba896a1e1d7b165759"},{"sha":"7d5ac0fac510fa5a8deec763688392e60ada514a","author":{"name":"jakirkham","email":"a65f82840b865057a74adf67d85c39540fb3eecd@gmail.com"},"message":"Merge pull request #99 from jakirkham/reg_rfft\n\nUse Real FFTs in Image Registration","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/7d5ac0fac510fa5a8deec763688392e60ada514a"},{"sha":"8f38b3e6c5f5669f9b41e781dad4f9c051799805","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Drop imports of `fftn` and `ifftn`\n\nAs the code only uses Real FFTs, there is no need to import and wrap\ncomplex FFT functions.","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/8f38b3e6c5f5669f9b41e781dad4f9c051799805"},{"sha":"e8e82cbe16fb607a1a053461438f072cad0612fb","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Drop explicit extraction of real FFT results\n\nIn the code, there were leftover calls to get the real part of the\nresult from `irfftn`. However `irfftn` already returns a real result. So\nthere is no imaginary part to strip off. As such, we can drop these\nrequests for the real part of the result as it is already satisfied.","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/e8e82cbe16fb607a1a053461438f072cad0612fb"},{"sha":"cde91e72d7128c48cac39d0b56b6b49119beb8c5","author":{"name":"jakirkham","email":"a65f82840b865057a74adf67d85c39540fb3eecd@gmail.com"},"message":"Merge pull request #100 from jakirkham/tidy_up_fft_real\n\nTidy up FFT usage","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/cde91e72d7128c48cac39d0b56b6b49119beb8c5"},{"sha":"fb9cb566bf678d540f6b1c4a64b2dd90023c20ac","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Add function to save TIFF file\n\nCan take any kind of array (including a Dask Array) and save it to the\nTIFF file specified (by filename).","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/fb9cb566bf678d540f6b1c4a64b2dd90023c20ac"},{"sha":"15ba68bd281e8412e3412fbe6c1f08975b0d025b","author":{"name":"jakirkham","email":"a65f82840b865057a74adf67d85c39540fb3eecd@gmail.com"},"message":"Merge pull request #101 from jakirkham/save_tiff_func\n\nAdd function to save TIFF file","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/15ba68bd281e8412e3412fbe6c1f08975b0d025b"},{"sha":"19253df3e0cfef29668dfd08b9f70c2c6e414c3a","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Switch workflow from Python 2 to Python 3\n\nUsers can still make use of Python 2 if they want. However it just makes\nsense at this point to use Python 3. It is newer, has many nice\nfeatures, and newer, more performant versions of our dependencies. Given\neverything we need can be installed on Python 3 (even optional\ndependencies), this is just the right way to go.","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/19253df3e0cfef29668dfd08b9f70c2c6e414c3a"},{"sha":"091862c291b8b57d9ffa73092f0a92b5b24a431f","author":{"name":"jakirkham","email":"a65f82840b865057a74adf67d85c39540fb3eecd@gmail.com"},"message":"Merge pull request #103 from jakirkham/use_py3\n\nSwitch workflow from Python 2 to Python 3","distinct":false,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/091862c291b8b57d9ffa73092f0a92b5b24a431f"},{"sha":"6df5619eaa6e3acd5b2583b664e784ff7eb3f925","author":{"name":"John Kirkham","email":"4f80d7f6884bed5b4eff8086948986c4f7dc5a5e@janelia.hhmi.org"},"message":"Switch from sge to lsf\n\nChange the workflow so that it launches ipyparallel to run on LSF\ninstead of SGE. Making this change because our work's cluster is\nchanging over to LSF.","distinct":true,"url":"https://api.github.com/repos/jakirkham/nanshe_workflow/commits/6df5619eaa6e3acd5b2583b664e784ff7eb3f925"}]}
{"actor":{"display_login":"jakirkham"}}