{"action":"created","issue":{"url":"https://api.github.com/repos/soft-matter/trackpy/issues/200","labels_url":"https://api.github.com/repos/soft-matter/trackpy/issues/200/labels{/name}","comments_url":"https://api.github.com/repos/soft-matter/trackpy/issues/200/comments","events_url":"https://api.github.com/repos/soft-matter/trackpy/issues/200/events","html_url":"https://github.com/soft-matter/trackpy/issues/200","id":54959498,"number":200,"title":"Multiple minor issues the the walkthru","user":{"login":"RobWardNZ","id":6218191,"avatar_url":"https://avatars.githubusercontent.com/u/6218191?v=3","gravatar_id":"","url":"https://api.github.com/users/RobWardNZ","html_url":"https://github.com/RobWardNZ","followers_url":"https://api.github.com/users/RobWardNZ/followers","following_url":"https://api.github.com/users/RobWardNZ/following{/other_user}","gists_url":"https://api.github.com/users/RobWardNZ/gists{/gist_id}","starred_url":"https://api.github.com/users/RobWardNZ/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RobWardNZ/subscriptions","organizations_url":"https://api.github.com/users/RobWardNZ/orgs","repos_url":"https://api.github.com/users/RobWardNZ/repos","events_url":"https://api.github.com/users/RobWardNZ/events{/privacy}","received_events_url":"https://api.github.com/users/RobWardNZ/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2015-01-21T00:09:07Z","updated_at":"2015-01-22T02:22:34Z","closed_at":null,"body":"Lots of easy documentation fixes......\r\n\r\nI am using Yosemite (OS X 10.10)\r\n\r\nOn this page: http://soft-matter.github.io/trackpy/tutorial/walkthrough.html\r\n\r\n1. The first line fails under ipython and python and on various versions (2.7 and 3.3):\r\n```\r\n%matplotlib inline\r\n```\r\n2. The \"print\" command also fails on py 3.3:\r\n```\r\nprint frames[0]  # the first frame\r\n```\r\nas it require parentheses:\r\n```\r\nprint (frames[0])  # the first frame\r\n```\r\n3. The print command also fails elsewhere on the page:\r\n```\r\nprint 'Before:', t['particle'].nunique()\r\nprint 'After:', t1['particle'].nunique()\r\n```\r\n4. The \"frames[0]\" command shows a plot in the documentation but it doesn't work in reality (elsewhere the plots seem to display fine as per the documentation).\r\n\r\n5. Py 2.7 does not appear to like this line:\r\n```\r\nframes = pims.ImageSequence('./sample_data/bulk_water/*.png', as_grey=True)\r\n```\r\nIt complains about converting to greyscale.\r\n\r\n6. I think it should be made explicitly clear in the documentation what python version the devs are using.  I have spent considerable time trying to use trackpy with py 3.4 which I could not make work.\r\n\r\n7. Install on py 3.4 fails:\r\n```\r\nconda install -c soft-matter trackpy\r\n\r\nFetching package metadata: ...\r\nSolving package specifications: ..\r\nError: Unsatisfiable package specifications.\r\nGenerating hint: \r\n[2/2                 ] |#######################################################################| 100%\r\n\r\nHint: the following combinations of packages create a conflict with the\r\nremaining packages:\r\n  - python 3.4*\r\n  - trackpy\r\n```\r\n8. These lines do not plot as shown in the walkthru:\r\n```\r\nd.plot()\r\ntm = tp.subtract_drift(t1, d)\r\ntp.plot_traj(tm)\r\n```\r\n9. To use .avi files we need to install FFMPEG. Details here: http://mikeboers.github.io/PyAV/\r\n```\r\nbrew install ffmpeg\r\n```\r\nReading video frames will fail at this stage:\r\n```\r\nframes = pims.Video('test5.avi', as_grey=True)\r\n\r\nImportError: This reader requires PyAV\r\n```\r\npip install av\r\n\r\nThis seems to work (py33) and does NOT require an \"import av\" to work with trackpy\r\n\r\n10. The \"edit on github\" link at the top of this page is broken: https://trackpy.readthedocs.org/en/latest/reference/trackpy.feature.html\r\n\r\nand the page itself needs formatting to make it clearer. e.g. this is all on one line:\r\n```\r\nimage : image array (any dimensions) diameter : feature size in px minmass : minimum integrated brightness  but should be:\r\n\r\nimage : image array (any dimensions) \r\ndiameter : feature size in px \r\nminmass : minimum integrated brightness\r\n\r\netc...\r\n```\r\n11. Same page..... Half way down the page, dataFrame is described but does not fit the flow of parameters.  I think this is the object that is returned, not a parameter that is passed to the object.\r\n\r\n12. Same page, \"preprocess\" is not highlighted.\r\n\r\n13. Same page.... \"engine\" and \"batch\" not highlighted, and what is \"batch\" anyway?\r\n\r\n14 I have edited the text to look like this for my own purposes (except for change of appearance upon pasting):\r\n```\r\n# trackpy.locate(\r\n# \traw_image,            image : image array (any dimensions)\r\n# \tdiameter,             diameter : feature size in px\r\n# \tminmass=100.0,        minmass : minimum integrated brightness\r\n#                         Default is 100, but a good value is often much higher. \r\n#                         This is a crucial parameter for elminating spurious features.\r\n# \tmaxsize=None,         maxsize : maximum radius-of-gyration of brightness, \r\n#                         default None\r\n# \tseparation=None,      separation : feature separation, in pixels.\r\n#                         Default is the feature diameter + 1\r\n# \tnoise_size=1,         noise_size : width of Gaussian blurring kernel, in pixels.\r\n#                         Default is 1. \r\n# \tsmoothing_size=None,  smoothing_size : size of boxcar smoothing, in pixels.\r\n#                         Default is the same is feature separation.        \r\n# \tthreshold=None,       threshold : Clip bandpass result below this value.\r\n#                         Default None, passed through to bandpass.\r\n# \tinvert=False,         invert : Set to True if features are darker than background. \r\n#                         False by default. \r\n# \tpercentile=64,        percentile : Features must have a peak brighter than pixels \r\n#                         in this percentile. This helps eliminate spurious peaks.  \r\n# \ttopn=None,            topn : Return only the N brightest features above minmass.\r\n#                         If None (default), return all features above minmass.\r\n# \tpreprocess=True,      preprocess : Set to False to turn out bandpass preprocessing.  \r\n# \tmax_iterations=10,    max_iterations : integer max number of loops to refine \r\n#                         the center of mass, default 10  \r\n# \tfilter_before=True,   filter_before : boolean. Use minmass (and maxsize, if set) \r\n#                         to eliminate spurious features based on their estimated mass \r\n#                         and size before refining position. True by default for performance.       \r\n# \tfilter_after=True,    filter_after : boolean. Use final characterizations of mass \r\n#                         and size to eliminate spurious features. True by default.      \r\n# \tcharacterize=True,    characterize : boolean. Compute “extras”: eccentricity, \r\n#                         signal, ep. True by default.      \r\n# \tengine=u'auto'        engine : {‘auto’, ‘python’, ‘numba’} \r\n# \t)\r\n#\r\n#   DataFrame([x, y, mass, size, ecc, signal]) where mass means total integrated \r\n#   brightness of the blob, size means the radius of gyration of its Gaussian-like\r\n#   profile, and ecc is its eccentricity (1 is circular).\r\n#\r\n```\r\n15. preprocess : Set to False to turn out bandpass preprocessing.\r\n```\r\n\"out\" or \"off\"?\r\n```\r\n16. Unclear what this means:\r\n```\r\ndiameter,             diameter : feature size in px\r\n```\r\nIs it a max, min, average...? What is the default?\r\n\r\n16. It is not clear to me what \"A\" is referring to in the following:\r\n\r\nIn water, a viscous material, the expected power-law exponent n=1. The value of A=4D, where D is the particles’ diffusivity. D is related to viscosity η, particle radius a, and temperature T as\r\n\r\nD=kT6πηa.\r\n\r\nFor paritcles with a 1 μm diameter in room-temperature water, A≈1.74. Our value above is not far off.\r\n\r\nTYPO in the above line: \"particles\".\r\n\r\n[TAC edited to add markup]"},"comment":{"url":"https://api.github.com/repos/soft-matter/trackpy/issues/comments/70961265","html_url":"https://github.com/soft-matter/trackpy/issues/200#issuecomment-70961265","issue_url":"https://api.github.com/repos/soft-matter/trackpy/issues/200","id":70961265,"user":{"login":"tacaswell","id":199813,"avatar_url":"https://avatars.githubusercontent.com/u/199813?v=3","gravatar_id":"","url":"https://api.github.com/users/tacaswell","html_url":"https://github.com/tacaswell","followers_url":"https://api.github.com/users/tacaswell/followers","following_url":"https://api.github.com/users/tacaswell/following{/other_user}","gists_url":"https://api.github.com/users/tacaswell/gists{/gist_id}","starred_url":"https://api.github.com/users/tacaswell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tacaswell/subscriptions","organizations_url":"https://api.github.com/users/tacaswell/orgs","repos_url":"https://api.github.com/users/tacaswell/repos","events_url":"https://api.github.com/users/tacaswell/events{/privacy}","received_events_url":"https://api.github.com/users/tacaswell/received_events","type":"User","site_admin":false},"created_at":"2015-01-22T02:22:34Z","updated_at":"2015-01-22T02:22:34Z","body":"Oh, yeah meant 'folder', not 'file'."}}