mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-24 22:21:43 +02:00
add typemaps and tests for numpy int arrays
+ some cleaning in the Python test and SWIG interface files
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@ -1,13 +1,12 @@
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import os
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import shutil
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#import numpy as np
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import numpy as np
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from pytrexio import *
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# TODO: make a user-friendly more pythonic API that will have to be autogenerated
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# add Exception handling
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# check of dimensions and call to safe API
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# conversion to and from numpy arrays
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# TODO:
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# 1) make a user-friendly more pythonic API that will have to be autogenerated
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# 2) add Exception handling (can be done easily in the front end python-ic API e.g. try: if function_call(...) == TREXIO_SUCCESS
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# automatically download (hopefully the latest version) numpy.i using
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# wget https://raw.githubusercontent.com/numpy/numpy/main/tools/swig/numpy.i
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@ -37,7 +36,7 @@ try:
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elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
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shutil.rmtree(output_filename)
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except:
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print (f'Test file {output_filename} does not exist')
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print ('Nothing to remove.')
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#=========================================================#
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#============ WRITE THE DATA IN THE TEST FILE ============#
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@ -50,14 +49,32 @@ nucleus_num = 12
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rc = trexio_write_nucleus_num(test_file, nucleus_num)
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assert rc==TREXIO_SUCCESS
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charges = doubleArray(nucleus_num)
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for i in range(nucleus_num):
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if i < nucleus_num/2:
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charges[i] = 6.
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else:
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charges[i] = 1.
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# initialize charge arrays as a list and convert it to numpy array
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charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
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charges_np = np.array(charges, dtype=np.float64)
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rc = trexio_write_nucleus_charge(test_file, charges)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemacs from numpy.i
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rc = trexio_write_safe_nucleus_charge(test_file, charges_np)
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assert rc==TREXIO_SUCCESS
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# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
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#charges = doubleArray(nucleus_num)
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#for i in range(nucleus_num):
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# if i < nucleus_num/2:
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# charges[i] = 6.
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# else:
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# charges[i] = 1.
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#rc = trexio_write_nucleus_charge(test_file, charges)
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# initialize arrays of nuclear indices as a list and convert it to numpy array
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indices = [i for i in range(nucleus_num)]
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# type cast is important here because by default numpy transforms a list of integers into int64 array
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indices_np = np.array(indices, dtype=np.int32)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemacs from numpy.i
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rc = trexio_write_safe_basis_nucleus_index(test_file, indices_np)
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assert rc==TREXIO_SUCCESS
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point_group = 'B3U'
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@ -97,43 +114,43 @@ test_file2 = trexio_open(output_filename, 'r', TEST_TREXIO_BACKEND)
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result = trexio_read_nucleus_num(test_file2)
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assert result[0]==TREXIO_SUCCESS
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assert result[1]==nucleus_num
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#print(result)
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charges2 = doubleArray(nucleus_num)
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print(charges2[3])
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#for i in range(nucleus_num):
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# charges2[i] = -1.
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rc = trexio_read_nucleus_charge(test_file2, charges2)
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assert rc==TREXIO_SUCCESS
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for i in range(nucleus_num):
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assert charges2[i]==charges[i]
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#charge_numpy = np.zeros(nucleus_num, dtype=np.float64)
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#print(charge_numpy)
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rc, charge_numpy = trexio_read_safe_nucleus_charge(test_file2, 12)
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print(charge_numpy)
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print(charge_numpy[11])
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# safe call to read_safe array of float values
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rc, rcharges_np = trexio_read_safe_nucleus_charge(test_file2, nucleus_num)
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assert rc==TREXIO_SUCCESS
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assert rcharges_np.dtype is np.dtype(np.float64)
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np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
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# unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM
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# but also should not return numpy array filled with garbage
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rc, charge_numpy = trexio_read_safe_nucleus_charge(test_file2, 12*5)
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#print(charge_numpy)
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# TODO: it should not return numpy array filled with garbage
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rc, rcharges_fail = trexio_read_safe_nucleus_charge(test_file2, nucleus_num*5)
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assert rc==TREXIO_UNSAFE_ARRAY_DIM
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# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
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#charges2 = doubleArray(nucleus_num)
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#for i in range(nucleus_num):
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# charges2[i] = -1.
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#rc = trexio_read_nucleus_charge(test_file2, charges2)
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#assert rc==TREXIO_SUCCESS
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#for i in range(nucleus_num):
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# assert charges2[i]==charges[i]
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# safe call to read_safe array of int values
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rc, rindices_np = trexio_read_safe_basis_nucleus_index(test_file2, nucleus_num)
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assert rc==TREXIO_SUCCESS
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assert rindices_np.dtype is np.dtype(np.int32)
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for i in range(nucleus_num):
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assert rindices_np[i]==indices_np[i]
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# [WIP]: ideally, the list of strings should be returned as below
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#rc, label_2d = trexio_read_nucleus_label(test_file2, 10)
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# [WIP]: currently only low-level routines (return one long string instead of an array of strings) work
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rc, labels_1d = trexio_read_nucleus_label_low(test_file2, 10)
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assert rc==TREXIO_SUCCESS
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labels_2d = [label for label in labels_1d.split(TREXIO_DELIM) if label]
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print(labels_2d)
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print('Read and parsed nuclear labels:\n', labels_2d)
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for i in range(nucleus_num):
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assert labels_2d[i]==labels[i]
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@ -10,32 +10,37 @@
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/* Include stdint to recognize types from stdint.h */
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%include <stdint.i>
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/* Include carrays to work with C pointers to arrays */
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/* NOTE:
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carrays was useful before numpy.i was introduced.
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For Python interface it's better to use numpy arrays instead of carrays, because the latter are less python-ic.
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On the other hand, carrays might be more portable to other target languages.
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// Include carrays to work with C pointers to arrays
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%include "carrays.i"
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/* Include classes that correspond to integer and float arrays */
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// Include classes that correspond to integer and float arrays
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%array_class(double, doubleArray);
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%array_class(float, floatArray);
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%array_class(int32_t, int32Array);
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%array_class(int64_t, int64Array);
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*/
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/* Include typemaps to play with input/output re-casting
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Useful when working with C pointers
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*/
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%include typemaps.i
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/* Redefine the int32_t* and int64_t* num to be output
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Useful for TREXIO read_num functions where the
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num variable is modified by address
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*/
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%apply int *OUTPUT { int32_t* const num};
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%apply int *OUTPUT { int64_t* const num};
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/* Does not work for arrays (SIGSEGV)
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%apply double *OUTPUT { double* const dataset };
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*/
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/* Does not work for arrays (SIGSEGV) */
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/* This enables access to trexio_[...]_read_dset_str_low set of functions
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in order to return one long string with TREXIO_DELIM delimeter as 2-nd argument of output tuple
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*/
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%include <cstring.i>
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%cstring_bounded_output(char* dset_out, 1024);
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%cstring_bounded_output(char* dset_out, 4096);
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/* [WIP] TREXIO back ends and exit codes can be redefined in the SWIG target language
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using %ignore and further #define statements (instead of disabling the type cast in the trexio.h file)
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@ -47,11 +52,11 @@
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#define TREXIO_TEXT 0
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*/
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/* This is an attempt to make SWIG treat double * dset_out, const uint64_t dim_out pattern
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/* This is an attempt to make SWIG treat double * dset_out|_in, int64_t dim_out|_in pattern
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as a special case in order to return the NumPy array to Python from C pointer to array
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provided by trexio_read_safe_[dset_num] function.
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NOTE: numpy.i is currently not part of SWIG but included in the numpy distribution (under numpy/tools/swig/numpy.i)
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This means that the interface file have to be provided to SWIG upon compilation either by
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This means that the interface file have to be provided to SWIG during compilation either by
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copying it to the local working directory or by providing -l/path/to/numpy.i flag upon SWIG compilation
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*/
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%include "numpy.i"
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@ -60,7 +65,12 @@
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import_array();
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%}
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/* Enable write|read_safe functions to convert numpy arrays from/to double arrays */
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%apply (double* ARGOUT_ARRAY1, int DIM1) {(double * const dset_out, const int64_t dim_out)};
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%apply (double* IN_ARRAY1, int DIM1) {(const double * dset_in, const int64_t dim_in)};
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/* Enable write|read_safe functions to convert numpy arrays from/to int32 arrays */
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%apply (int* ARGOUT_ARRAY1, int DIM1) {(int32_t * const dset_out, const int64_t dim_out)};
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%apply (int* IN_ARRAY1, int DIM1) {(const int32_t * dset_in, const int64_t dim_in)};
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/* This tells SWIG to treat char ** dset_in pattern as a special case
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Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.
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@ -93,47 +103,7 @@ import_array();
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free((char *) $1);
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}
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/* [WIP] This is an attempt to make SWIG treat char ** dset_out as a special case
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In order to return list of string to Python from C-native char ** dset_out,
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which is modified (but not allocated) within the trexio_[...]_read_dset_str function
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*/
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%typemap(in, numinputs=0) char ** dset_out (char * temp) {
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/*temp = (char *) malloc(1028*sizeof(char));*/
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$1 = &temp;
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}
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%typemap(argout) char ** dset_out {
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Py_ssize_t i = 0;
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Py_ssize_t mysize = 12;
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PyObject *o_res = PyList_New(mysize);
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PyObject *o;
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for (i = 0; i < mysize; i++) {
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//printf("%s\n", $1[i]);
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o = PyString_FromString($1[i]);
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PyList_SetItem(o_res, i, o);
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}
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PyObject *o2, *o3;
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if ((!$result) || ($result == Py_None)) {
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$result = o_res;
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} else {
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if (!PyTuple_Check($result)) {
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PyObject *o2 = $result;
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$result = PyTuple_New(1);
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PyTuple_SetItem($result, 0, o2);
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}
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o3 = PyTuple_New(1);
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PyTuple_SetItem(o3, 0, o_res);
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o2 = $result;
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$result = PySequence_Concat(o2, o3);
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Py_DECREF(o2);
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Py_DECREF(o3);
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Py_DECREF(o_res);
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}
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}
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/* Parse the header files to generate wrappers */
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%include "trexio_s.h"
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%include "trexio.h"
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