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July 23, 2018 10:25
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Mapping the 2D array of burn days to a True/False voxelspace
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| # Plain for loops | |
| import numpy as np | |
| for j in range(one_month_data.shape[1]): | |
| for i in range(one_month_data.shape[0]): | |
| if not np.isnan(one_month_data[i,j]): | |
| voxelspace[int(one_month_data[i,j]), i, j] = True if one_month_data[i,j] > 0 else False | |
| elif np.isnan(one_month_data[i,j]); | |
| date_start, date_end = get_dates_for_current_month() # return integers | |
| voxelspace[date_start:date_end, i, j] = np.nan | |
| elif one_month_data[i,j] == 0; | |
| date_start, date_end = get_dates_for_current_month() | |
| voxelspace[date_start:date_end, i, j] = False | |
| # Cythonised version | |
| import cython | |
| cimport numpy | |
| from libc.math cimport isnan | |
| cdef float NAN | |
| NAN = float("NaN") | |
| # Or use a NoData vlue | |
| cdef int NoData = -9999 | |
| # set up ctypes for the variables in the function to allow it to cythonise nicely | |
| cdef int i = 0 | |
| cdef int j = 0 | |
| cdef int jmax = one_month_data.shape[1] | |
| cdef int imax = one_month_data.shape[0] | |
| # Best to turn off these decorators if you are debugging | |
| # (Segfaults etc.) | |
| @cython.boundscheck(False) | |
| @cython.wraparound(False) | |
| @cython.nonecheck(False) | |
| def voxelspace(np.ndarray[DTYPE_t, ndim=3] voxelspace, np.ndarray[DTYPE_t, ndim=2] one_month_data, MORE_ARGS...): | |
| for j in range(jmax): | |
| for i in range(imax): | |
| if not isnan(one_month_data[i,j]): | |
| voxelspace[int(one_month_data[i,j]), i, j] = True if one_month_data[i,j] > 0 else False | |
| elif np.isnan(one_month_data[i,j]); | |
| date_start, date_end = get_dates_for_current_month() # return C-type integers from this function | |
| voxelspace[date_start:date_end, i, j] = NAN # Or NoData value | |
| elif one_month_data[i,j] == 0; | |
| date_start, date_end = get_dates_for_current_month() | |
| voxelspace[date_start:date_end, i, j] = False | |
| return voxelspace | |
| def get_dates_for_current_month(month): | |
| #...code here | |
| cdef int start_date | |
| cdef int end_date | |
| # More code.... | |
| return start_date, end_date | |
| # Add in later paralelism once working: | |
| with nogil, parallel(num_threads=num_threads_use): | |
| # OpenMP threads created for the outer loop. | |
| for i in prange(jmax): | |
| # etc...... |
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@DTMilodowski points out
np.isfinitewould get rid of theis notformation 👍