{
    "info": {
        "author": "Thomas Ryan-Keogh, Charlotte Robinson",
        "author_email": "tjryankeogh@gmail.com",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "Phytoplankton Photophysiology Utils\n===================================\n\nThis is a tool to read and process active chlorophyll fluorescence data from raw format and apply the biophysical model of Kolber et al. (1998).\nFor more information see the documentation and demo file, below is a short example of how to use the data to read in and process variables.\n\n\nEXAMPLE USAGE\n-------------\nThis package is meant to be used in an interactive environment - ideally Jupyter Notebook\n\n```python\nimport phyto_photo_utils as ppu\n\nfname = '/path_to_data/data'\noutput = '/output_path'\n\n# Load all variables needed for fitting saturation and relaxation models\ndf = ppu.load_FASTTrackaI_files(fname, append=False, save_files=True, res_path=output, seq_len=120, irrad=545.62e10)\n\n# Perform a \u03c1 saturation model fit on the data\nsat = ppu.fit_saturation(pfd, fyield, seq, datetime, blank=0, sat_len=100, skip=0, ro_lims=[0.0,1.0], sig_lims =[100,2200])\n\n# Perform a single decay relaxation model fit on the data\nrel = ppu.fit_single(fyield, seq_time, seq, datetime, blank=0, sat_len=100, rel_len=40, single_decay=True, bounds=True, tau_lims=[100, 50000])\n\n# Perform time averaging (5 minute averages) on raw transients, including the removal of outliers (mean + stdev * 3)\ndfm = ppu.remove_outlier_from_time_average(df, time=5, multiplier=3)\n\n# Correct for FIRe instrument detector bias\ndfb = ppu.correct_fire_instrument_bias(df, sat=False, pos=1, sat_len=100)\n\n# See the demo file for more info\n```\n\n\nABOUT\n-----\nThis work was funded by the CSIR. This research was partially supported by the Australian Government through the Australian Research Council's Discovery Projects funding scheme (DP160103387).\n\n- Version: 1.1\n- Author:  Thomas Ryan-Keogh, Charlotte Robinson\n- Email:   tjryankeogh@gmail.com\n- Date:    2018-12-06\n- Institution: Council for Scientific and Industrial Research, Curtin University\n- Research group: Southern Ocean Carbon - Climate Observatory (SOCCO), Remote Sensing and Satellite Research Group\n\nPlease use the guidlines given on https://integrity.mit.edu/handbook/writing-code to cite this code.\n\n**Example citation:**\nSource: phyto_photo_utils [https://gitlab.com/socco/BuoyancyGliderUtils](https://gitlab.com/tjryankeogh/phytophotoutils) retrieved on 30 May 2019.\n\nPACKAGE STRUCTURE\n-----------------\nNOTE: This package structure is defined by the `__init__.py` file\n- load\n\t- load_FIRe_files\n\t- load_FASTTrackaI_files\n\t- load_FastOcean_files\n- saturation\n\t- fit_saturation\n- relaxation\n\t- fit_relaxation\n- tools\n\t- remove_outlier_from_time_average\n\t- correct_fire_instrument_bias\n\t- calculate_blank_FastOcean\n\t_ calculate_blank_FIRe\n- spectral_correction\n\t- calculate_chl_specific_absorption\n\t- calculate_instrument_led_correction\n- flc\n\t- calculate_etr\n- plot\n\t- plot_saturation_data\n\t- plot_relaxation_data\n\t- plot_fluorescence_light_curve\n- equations\n\t- __fit_kolber_nop__\n\t- __calculatate_residual_saturation_nop__\n\t- __fit_kolber_p__\n\t- __calculate_residual_saturation_p__\n\t- __fit_single_relaxation__\n\t- __calculate_residual_single_relaxation__\n\t- __fit_triple_relaxation__\n\t- __calculate_residual_triple_relaxation__\n\t- __calculate_Webb_model__\n\t- __calculate_residual_etr__\n\t- __calculate_modified_Webb_model__\n\t- __calculate_residual_phi__\n\t- __calculate_rsquared__\n\t- __calculate_bias__\n\t- __calculate_chisquared__\n\t- __calculate_reduced_chisquared__\n\t- __calculate_rmse__\n\t- __calculate_fit_errors__\n- fitting\n\t- __fit_fixed_p_model__\n\t- __fit_calc_p_model__\n\t- __fit_no_p_model__\n\t- __fit_single_decay__\n\t- __fit_triple_decay__\n\n\nACKNOWLEDGEMENTS\n----------------\n- Kevin Oxborough (Chelsea Technology Groups) for linear methods to estimate Fo and Fm\n\n\nTO DO\n-----\n- Add in function to read FastTracka I binary files\n- Add deconvolution method for triple decay relaxation\n- Add the option using different production models in FLC processing\n- Add methods to load in discrete FIRe files\n- Add additional load methods for newer FIRe instruments\n- Add additional load method for FastTracka II\n- Add additional load method for Soliense LIFT-FRR\n- Add additional load method for CTG LabSTAF",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "https://gitlab.com/tjryankeogh/phytophotoutils/-/archive/v1.1/phytophotoutils-v1.1.tar.gz",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://gitlab.com/tjryankeogh/phytophotoutils",
        "keywords": "",
        "license": "MIT License",
        "maintainer": "",
        "maintainer_email": "",
        "name": "phyto-photo-utils",
        "package_url": "https://pypi.org/project/phyto-photo-utils/",
        "platform": "",
        "project_url": "https://pypi.org/project/phyto-photo-utils/",
        "project_urls": {
            "Download": "https://gitlab.com/tjryankeogh/phytophotoutils/-/archive/v1.1/phytophotoutils-v1.1.tar.gz",
            "Homepage": "https://gitlab.com/tjryankeogh/phytophotoutils"
        },
        "release_url": "https://pypi.org/project/phyto-photo-utils/1.1/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "Tools and utilities for active chlorophyll fluorescence data processing.",
        "version": "1.1"
    },
    "last_serial": 5977675,
    "releases": {
        "1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "2c33a2fa832a756bc2dc9e31f6fef27e",
                    "sha256": "f2146295f6b05dc3c1b2a3f5a0f00baef44c273ff0850f34b27874613fdf0263"
                },
                "downloads": -1,
                "filename": "phyto_photo_utils-1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "2c33a2fa832a756bc2dc9e31f6fef27e",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20729,
                "upload_time": "2019-10-03T13:54:53",
                "url": "https://files.pythonhosted.org/packages/4d/9a/717ca59750ba277b02cd22d2be93373b34a627c12aa7f2fcb14569158f20/phyto_photo_utils-1.0.tar.gz"
            }
        ],
        "1.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "bc235c13a40e1d6fd1697a4a965976d3",
                    "sha256": "ffd962c6602aacf490a34ce38ed23754a87be2d01ee5dd88732bfd14a0b1733e"
                },
                "downloads": -1,
                "filename": "phyto_photo_utils-1.0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "bc235c13a40e1d6fd1697a4a965976d3",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20738,
                "upload_time": "2019-10-03T14:00:24",
                "url": "https://files.pythonhosted.org/packages/85/73/12cbcd162ae79467c06464c46242c7cf497a7f1dc985d0db7cb7d5137030/phyto_photo_utils-1.0.1.tar.gz"
            }
        ],
        "1.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "00043c09f7642e0c5f94f977023e13af",
                    "sha256": "4554b9a7d61e374431643b44ef319881f1f1df3d5ea2355e9815a35cd243a4ae"
                },
                "downloads": -1,
                "filename": "phyto_photo_utils-1.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "00043c09f7642e0c5f94f977023e13af",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20708,
                "upload_time": "2019-10-06T15:17:13",
                "url": "https://files.pythonhosted.org/packages/1c/d9/e9bf49ae502d58e37523f889dc2f75439ac1c8f874998de335206b498dda/phyto_photo_utils-1.0.2.tar.gz"
            }
        ],
        "1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0754c018ba13cda61ea8144dd56c3adb",
                    "sha256": "c5d872a04c51b56a0e204a31892981bd0dfc81be93697134c1567bbcad4d47c0"
                },
                "downloads": -1,
                "filename": "phyto_photo_utils-1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "0754c018ba13cda61ea8144dd56c3adb",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20614,
                "upload_time": "2019-10-15T14:31:19",
                "url": "https://files.pythonhosted.org/packages/51/ac/815d9598eb265426361698feb260b4a78e588c2d663c752451b30a3b6f56/phyto_photo_utils-1.1.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "0754c018ba13cda61ea8144dd56c3adb",
                "sha256": "c5d872a04c51b56a0e204a31892981bd0dfc81be93697134c1567bbcad4d47c0"
            },
            "downloads": -1,
            "filename": "phyto_photo_utils-1.1.tar.gz",
            "has_sig": false,
            "md5_digest": "0754c018ba13cda61ea8144dd56c3adb",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 20614,
            "upload_time": "2019-10-15T14:31:19",
            "url": "https://files.pythonhosted.org/packages/51/ac/815d9598eb265426361698feb260b4a78e588c2d663c752451b30a3b6f56/phyto_photo_utils-1.1.tar.gz"
        }
    ]
}