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Merging Dev1.6 for the upcoming hoki v1.6 release #76
Commits on Jun 2, 2020
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Created CSP archistecture and basic sfh class
The complex stellar population subpackage is meant to combine bpass variables with a stelalr formation history to generate more complex populations. To this end, we're implementing a stellar formation history class. The basic SFH class for custom SFH is implemented using scipy splines. This basic class is also tested.
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Commits on Jun 5, 2020
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Commits on Jun 9, 2020
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Adds
at_time
function to the event rate classThis method allows for the calculation of the event rate at a given lookback time. It uses the BPASS binning for this. This method is much faster, but suffers from a lack of accuracy.
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Commits on Jun 10, 2020
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Commits on Jun 11, 2020
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Implements calculate spectrum at_time and over_time functions
Both functions are implemented for the BPASS spectra. However, the method is similar to the BPASS event rate calculation, which is sub optimal for the spectra calculation. It takes an extremely long time to do the calculation. A for loop of 100000 iterations is present, because each wavelength is seen as it's own "event type". It should be possible to remove this by implementing a function to take the separate wavelengths as a single unit. It would be interesting so see the influence of putting the for loop within a numba function, but thinking about restructuring the function is probably better. Including a "caching" of the BPASS spectra into a pickled DataFrame. Additional test files are required for this to run.
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Commits on Jun 16, 2020
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Commits on Jun 18, 2020
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Commits on Jun 19, 2020
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expanded on the starcounts.py tests and put them in the right place +…
… added TypeError catch
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Adjust eventrate functions to take lists of functions
Instead of requiring a scipy interpolated spline as input. These functions now take a list of functions as input for the stellar formation and metallicity history. This adjustment has been made by using `numpy.interp` instead of scipy.interpolate. Furthermore, instead of scipy's spline integration `numpy.trapz` is now used to calculate the mass per bin.
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Commits on Jun 21, 2020
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Commits on Jun 22, 2020
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Commits on Jun 23, 2020
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Commits on Jun 24, 2020
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- Adds BPASS IMFS to the constants - Adds check to BPASS IMFS - Adds test for `data_compiler.SpectraData` - Reduces data usage for rate tests
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Commits on Jun 26, 2020
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Uses `unittest.mock` to allow for a smaller DataFrame to be used.
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Commits on Jun 28, 2020
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Commits on Jun 30, 2020
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The compiler now outputs the BPASS spectra as a 3D `numpy.ndarray` this minimises storage and allows for faster and less memory hungry operations than the MultiIndex pandas DataFrame. The tests are updated accordingly and using unittest.mock a single spectra file is use. (This could be simulated too)
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Documentation update + SFH input
The documentation now shows the size and shape of each input and output variable. The `_over_time` and `_at_time` for `CSPSpectra` and `CSPEventRate` are now able to take the `SFH` object as an input.
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Removed CSP from utils due to cyclical import
The CSP class in `utils` was importing the SFH class, which was importing the `utils` module. Therefore, failing importing. Thus, the CSP class has been moved to a separate file
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Commits on Jul 1, 2020
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Commits on Jul 8, 2020
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Commits on Jul 10, 2020
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Commits on Jul 16, 2020
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at_time new default sample rate + load functions moved to hoki.load
at_time now uses 1000 as the default sample rate. The BPASS bins can still be used is a negative number is given. The `load_spectra` and `load_rates` have been moved to `hoki.load` and renamed to `all_spectra` and `all_rates`, respectively. tests have been adjusted accordingly
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Commits on Jul 31, 2020
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private optimised mass_per_time_bin calculation
Implements 2 new functions: - A custom numba trapezoidal function - A optimised mass_per_bin function for non-function-based data
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Refactored Event Rate calculation from array data
The original event rate calculation took functions as in input. This becomes cumbersome when you have data at specific time values. This calculation is done by taking a 2D matrix with time points on one axis and BPASS metallicities on the other. The values of the matrix describes the SFR at that moment in time. The calculate_rate_over_time function has been adjusted to use this new function.
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Commits on Aug 6, 2020
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Martin Glatzle committed
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Commits on Aug 25, 2020
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Martin Glatzle committed
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Commits on Aug 26, 2020
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Merge pull request #58 from findesgh/csp
Small bugfix in `all_spectra` The binary `kwarg` was not passed on to `SpectraCompiler` from `load.all_spectra`.
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Commits on Aug 27, 2020
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Commits on Aug 28, 2020
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BUG: use np instead of pd in SpectraCompiler.
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BUG: fix index and make test pass.
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BUG: fix another regression bug.
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Merge branch 'csp' of https://github.com/HeloiseS/hoki into csp_fix2
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Martin Glatzle committed
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Updates mass per bin calculation for vectorized funciton input
mass_per_bin now takes a normal python callable and a vectorized function as input. The latter boosts performance significantly
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Renames CSPEventRate functions and adds grid functions
- CSPEventRate functions are now called: - calculate_rate_over_time -> over_time - calculate_rate_at_time -> at_time new functions: - grid_over_time: calculates the rates from a 2D SFH (per BPASS metallicity) from time_points to time bins - grid_at_time: calculate the event rate at a specific moment in lookback time from a 2D SFH grid
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Merge pull request #60 from findesgh/csp_fix2
* BUG: use np instead of pd in SpectraCompiler. * BUG: fix index and make test pass. * BUG: fix another regression bug. * Fix further regression bug. Authored-by: Martin Glatzle <mglatzle@mpa-garching.mpg.de>
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Commits on Aug 29, 2020
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Set default sample rate for at_time
Also includes some docstring updates
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Adds grid functions for the spectra calculation
CSPSpectra now has the following functions: Public: - at_time: at time with function input - over_time: over lb time with function input - grid_at_time: at time with SFH grid input - grid_over_time: over lb time with SFH grid input Private: - grid_rate_calculator_at_time - grid_rate_calculator_over_time The grid_rate_calculators_* are numba functions that have the grid_* around them as wrappers for the input and output
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Commits on Aug 31, 2020
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Commits on Sep 21, 2020
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Bug fix in nr_time_bins (grid_over_time functions)
Instead of N bins being created, N-1 bin was being created.
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Commits on Oct 4, 2020
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File check, combined data_compiler tests, renames func+variables
renamed variables: - BPASS_METALLICITIES. now with `z` renamed functions: - all_rates -> rates_all_z - all_spectra -> spectra_all_z
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Commits on Oct 5, 2020
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Complex Stellar Populations (#64)
This submodule introduces the possibility to create Complex Stellar Populations with BPASS data. The two main modules are `csp.eventrate` and `csp.spectra` `csp.eventrate` contains the `CSPEventRate` class, which can be used to calculate event rates from a given Stellar Formation History and Metallicity evolution. The following methods are available in this class: `at_time`: calculates the event rates at a given lookback time. `over_time`: calculates the event rates over a lookback time (binned). `grid_at_time`: alternative input. Takes a grid of points instead of a function. Does the same as at_time. `grid_over_time`: alternative input. Takes a grid of points instead of a function. Does the same as over_time. `csp.spectra` contains the `CSPSpectra` class, which can be used to calculate synthetic spectra for the given population. The same methods are available in this class as `CSPEventRate`, but provide spectra rather than even rates. `csp.sfh` contains a class with which a Stellar Formation History (SFH) can be made. A collection of common parametric SFH are available (see documentation), but a custom one can also be given. As support for these high level functions, a collection of utility and helper functions has been added. These can be found in `csp.utils`. Some these are optimised for performance (`numba` JIT compiled) and are not user friendly. * Created CSP archistecture and basic sfh class * Added variables to constants * implements utility functions & new test files * Implements event rate calculation over time * BPASS data_files for testing file_loading * Adds `at_time` function to the event rate class * Adds docstrings and extra tests * Implements calculate spectrum at_time and over_time functions * Add normalisation function for the BPASS spectrum * fixed hrd plot * adding csp folder * minor changes * Moved tests to CSP folder + fix in function name _type_check * added a hokitype error * Added some code review for Max and minor stylistic changes * Added some code review for Max and minor stylistic changes * Updated the tests * bla * Adjust tests and docstrings * Adjust eventrate functions to take lists of functions * Disabled spectra test * Added parametric star formation histories to SFH and refactored some variable names * fixing CI * Auto stash before merge of "csp" and "official_hoki/csp" * upload files for remote work * Improve testing and functions * Add SpectraCompiler test * Adds extensive tests for the CSP package * Update SpectraCompiler * Documentation update + SFH input * Removed CSP from utils due to cyclical import * Updated setup.cfg to include csp_test_data subfolder * Removes leftover print statement + prints loading precompiled failed * Correct metallicity mid-points * Added the parametric star formation histories as public functions * at_time new default sample rate + load functions moved to hoki.load * Fixed typo * Removes cyclical import * Adjusted tests that use SpectraCompiler * Getting tox to work * private optimised mass_per_time_bin calculation * Refactored Event Rate calculation from array data * Removed dependency and added more doc information * BUG: pass on kwarg to spectra compiler. * Fix SpectraCompiler * BUG: use np instead of pd in SpectraCompiler. * BUG: fix index and make test pass. * BUG: fix another regression bug. * Fix further regression bug. * Clean up loading module * Updates mass per bin calculation for vectorized funciton input * Renames CSPEventRate functions and adds grid functions * np.zeros to np.empty where possible * Fixed incorrect test of at_time and over_time * Set default sample rate for at_time * Adds `cache` parameter to over_time_spectrum * Adds grid functions for the spectra calculation * Adds return_time_edges to grid_over_time & bug fix sfh vectorisation * Bug fix in nr_time_bins (grid_over_time functions) * Docs string cleanup * Solve cyclical import error * Fix tox and remove corner plot * File check, combined data_compiler tests, renames func+variables Co-authored-by: Max Briel <max.briel@auckland.ac.nz> Co-authored-by: heloises <heloisefw@gmail.com> Co-authored-by: Heloise <HeloiseS@users.noreply.github.com> Co-authored-by: findesgh <findessp@yandex.ru> Co-authored-by: Martin Glatzle <mglatzle@mpa-garching.mpg.de>
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Commits on Oct 6, 2020
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Emissivity compiling and loading. (#62)
* Created CSP archistecture and basic sfh class * Added variables to constants * implements utility functions & new test files * Implements event rate calculation over time * BPASS data_files for testing file_loading * Adds `at_time` function to the event rate class This method allows for the calculation of the event rate at a given lookback time. It uses the BPASS binning for this. This method is much faster, but suffers from a lack of accuracy. * Adds docstrings and extra tests * Implements calculate spectrum at_time and over_time functions Both functions are implemented for the BPASS spectra. However, the method is similar to the BPASS event rate calculation, which is sub optimal for the spectra calculation. It takes an extremely long time to do the calculation. A for loop of 100000 iterations is present, because each wavelength is seen as it's own "event type". It should be possible to remove this by implementing a function to take the separate wavelengths as a single unit. It would be interesting so see the influence of putting the for loop within a numba function, but thinking about restructuring the function is probably better. Including a "caching" of the BPASS spectra into a pickled DataFrame. Additional test files are required for this to run. * Add normalisation function for the BPASS spectrum * fixed hrd plot * adding csp folder * minor changes * Moved tests to CSP folder + fix in function name _type_check * added a hokitype error * Added some code review for Max and minor stylistic changes * Added some code review for Max and minor stylistic changes * Updated the tests * bla * Adjust tests and docstrings * Adjust eventrate functions to take lists of functions Instead of requiring a scipy interpolated spline as input. These functions now take a list of functions as input for the stellar formation and metallicity history. This adjustment has been made by using `numpy.interp` instead of scipy.interpolate. Furthermore, instead of scipy's spline integration `numpy.trapz` is now used to calculate the mass per bin. * Disabled spectra test * Added parametric star formation histories to SFH and refactored some variable names * fixing CI * Auto stash before merge of "csp" and "official_hoki/csp" * upload files for remote work * Improve testing and functions - Adds BPASS IMFS to the constants - Adds check to BPASS IMFS - Adds test for `data_compiler.SpectraData` - Reduces data usage for rate tests * Add SpectraCompiler test Uses `unittest.mock` to allow for a smaller DataFrame to be used. * Adds extensive tests for the CSP package * Update SpectraCompiler The compiler now outputs the BPASS spectra as a 3D `numpy.ndarray` this minimises storage and allows for faster and less memory hungry operations than the MultiIndex pandas DataFrame. The tests are updated accordingly and using unittest.mock a single spectra file is use. (This could be simulated too) * Documentation update + SFH input The documentation now shows the size and shape of each input and output variable. The `_over_time` and `_at_time` for `CSPSpectra` and `CSPEventRate` are now able to take the `SFH` object as an input. * Removed CSP from utils due to cyclical import The CSP class in `utils` was importing the SFH class, which was importing the `utils` module. Therefore, failing importing. Thus, the CSP class has been moved to a separate file * Updated setup.cfg to include csp_test_data subfolder * Removes leftover print statement + prints loading precompiled failed * Correct metallicity mid-points * Added the parametric star formation histories as public functions * at_time new default sample rate + load functions moved to hoki.load at_time now uses 1000 as the default sample rate. The BPASS bins can still be used is a negative number is given. The `load_spectra` and `load_rates` have been moved to `hoki.load` and renamed to `all_spectra` and `all_rates`, respectively. tests have been adjusted accordingly * Fixed typo * Removes cyclical import * Adjusted tests that use SpectraCompiler * Getting tox to work * private optimised mass_per_time_bin calculation Implements 2 new functions: - A custom numba trapezoidal function - A optimised mass_per_bin function for non-function-based data * Refactored Event Rate calculation from array data The original event rate calculation took functions as in input. This becomes cumbersome when you have data at specific time values. This calculation is done by taking a 2D matrix with time points on one axis and BPASS metallicities on the other. The values of the matrix describes the SFR at that moment in time. The calculate_rate_over_time function has been adjusted to use this new function. * Removed dependency and added more doc information * BUG: pass on kwarg to spectra compiler. * Fix SpectraCompiler * BUG: use np instead of pd in SpectraCompiler. * BUG: fix index and make test pass. * BUG: fix another regression bug. * Fix further regression bug. * Clean up loading module * Updates mass per bin calculation for vectorized funciton input mass_per_bin now takes a normal python callable and a vectorized function as input. The latter boosts performance significantly * Renames CSPEventRate functions and adds grid functions - CSPEventRate functions are now called: - calculate_rate_over_time -> over_time - calculate_rate_at_time -> at_time new functions: - grid_over_time: calculates the rates from a 2D SFH (per BPASS metallicity) from time_points to time bins - grid_at_time: calculate the event rate at a specific moment in lookback time from a 2D SFH grid * np.zeros to np.empty where possible * Fixed incorrect test of at_time and over_time * Set default sample rate for at_time Also includes some docstring updates * Adds `cache` parameter to over_time_spectrum * Adds grid functions for the spectra calculation CSPSpectra now has the following functions: Public: - at_time: at time with function input - over_time: over lb time with function input - grid_at_time: at time with SFH grid input - grid_over_time: over lb time with SFH grid input Private: - grid_rate_calculator_at_time - grid_rate_calculator_over_time The grid_rate_calculators_* are numba functions that have the grid_* around them as wrappers for the input and output * Adds return_time_edges to grid_over_time & bug fix sfh vectorisation * Emissivity compiling and loading. * Rename func, add existence of metallicity files, remove try/except Try/except has been replace by a if/else with a file check. * Finalise merge of `origin/dev1.6` into `data_loading` Co-authored-by: Max Briel <max.briel@auckland.ac.nz> Co-authored-by: heloises <heloisefw@gmail.com> Co-authored-by: Max Briel <max.briel@gmail.com> Co-authored-by: Heloise <HeloiseS@users.noreply.github.com> Co-authored-by: Max <14039563+maxbriel@users.noreply.github.com> Co-authored-by: Martin Glatzle <mglatzle@mpa-garching.mpg.de>
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REFACTOR: bin_spectra to bin_luminosity.
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REFACTOR: move binning utils to spec.
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Merge pull request #52 from findesgh/rebin
Utils for binning of spectra (in luminosity space)
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Heloise committed
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Merge pull request #72 from HeloiseS/agewizard_errors
Agewizard errors
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Merge branch 'dev1.6' of https://github.com/HeloiseS/hoki into dev1.6
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Merge branch 'dev1.6' of https://github.com/HeloiseS/hoki into dev1.6
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* Installs the requested python version (3.6 and 3.7) and uses `tox-gh-actions` to run the correct tox versions. * self import in `hoki.age.utils` fixed. * Add init files in test folders to account for similarly named test files.
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added nsamples to agewizard and docstrings missing in age.utils
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Merge pull request #75 from HeloiseS/csp_prerelease
Complex Stellar Populations
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