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-* Todo list for the binary_c-python
-** Logging functionality:
-Idea is to be able to give a string via python that will be used in the through the libbinary_c.so so that log_every_timestep.c
-
-** General:
-*** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
- CLOSED: [2019-10-29 Tue 17:44]
-*** DONE make routine that reads out all the lines, splits them into pieces and reads out the correct key
- CLOSED: [2019-10-29 Tue 17:43]
-*** TODO Put header and other source files in a dedicated directory
-*** TODO Use sphinx or read the docs for auto generation of documentation
-*** TODO Have the compiled files put into a build directory
-*** TODO add pythonpath thing to readme
-*** TODO make script that will set up binaryc automatically so that this can become an out of the box thing
-*** TODO Test the importing of this code from different places
-** Population ideas
-*** TODO Queuing system and some multiprocessing to run many systems
-*** TODO Consider rewriting the work that perl does
diff --git a/.#TODO.org b/.#TODO.org
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-david@david-Lenovo-IdeaPad-S340-14IWL.21326:1572369068
\ No newline at end of file
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* Todo list for the binary_c-python
** Logging functionality:
-Idea is to be able to give a string via python that will be used in the
+*** Idea
+Idea is to be able to give a string via python that will be used in the through the libbinary_c.so so that log_every_timestep.c
+The code below is the piece in log_every_timestep that uses it.
+ if(stardata->preferences->custom_output_function != NULL)
+ {
+ Dprint("calling custom output function %p\n",
+ stardata->preferences->custom_output_function);
+ stardata->preferences->custom_output_function(stardata);
+ }
+
+So the function should recieve 'stardata' as input.
+
+We can do that with providing a logging string alltogether, or generate a logging function
+
+In either way, this should be passed to stardata->preferences->custom_output_function as a pointer to that function
+
+
+*** Provide string for logging
+In perl this is done in the following way:
+
+sub binary_c_log_code
+{
+ my ($code) = @_;
+ return "
+#pragma push_macro(\"MAX\")
+#pragma push_macro(\"MIN\")
+#undef MAX
+#undef MIN
+#include \"binary_c.h\"
+
+void custom_output_function(SV * x);
+SV * custom_output_function_pointer(void);
+
+SV * custom_output_function_pointer()
+{
+ /*
+ * use PTR2UV to convert the function pointer
+ * &custom_output_function to an unsigned int,
+ * which is then converted to a Perl SV
+ */
+ return (SV*)newSVuv(PTR2UV(&custom_output_function));
+}
+
+void custom_output_function(SV * x)
+{
+ struct stardata_t * stardata = (struct stardata_t *)x;
+ $code;
+}
+#undef MAX
+#undef MIN
+#pragma pop_macro(\"MIN\")
+#pragma pop_macro(\"MAX\")
+";
+}
+
+And then to use it via
+ $population->set(
+ C_logging_code => '
+ PRINTF("MY_STELLAR_DATA %g %g %g %g\n",
+ stardata->model.time,
+ stardata->star[0].mass,
+ stardata->model.probability,
+ stardata->model.dt);
+ '
+ );
+
+Or use it via:
+
+*** auto logging
+We should also try to be able to have the code autogenerate some logging function via the following:
+
+$population->set( C_auto_logging => {
+ 'MY_STELLAR_DATA' =>
+ [
+ 'model.time',
+ 'star[0].mass',
+ 'model.probability',
+ 'model.dt'
+ ]
+ });
+
+
+Which is handled in perl via (see binary_grid2.pm
+sub autogen_C_logging_code
+{
+ # given a hash of arrays of variable names, where the hash
+ # key is the header, autogenerate PRINTF statements
+ my ($self) = @_;
+ my $code = undef;
+ if(defined $self->{_grid_options}->{C_auto_logging} &&
+ ref $self->{_grid_options}->{C_auto_logging} eq 'HASH'
+ )
+ {
+ $code = '';
+
+ foreach my $header (keys %{$self->{_grid_options}->{C_auto_logging}})
+ {
+ if(ref $self->{_grid_options}->{C_auto_logging}->{$header} eq 'ARRAY')
+ {
+ $code .= 'PRINTF("'.$header.' ';
+ foreach my $x (@{$self->{_grid_options}->{C_auto_logging}->{$header}})
+ {
+ $code .= '%g ';
+ }
+ $code .= '\n"';
+
+ foreach my $x (@{$self->{_grid_options}->{C_auto_logging}->{$header}})
+ {
+ $code .= ',((double)stardata->'.$x.')';
+ }
+ $code .= ');'
+ }
+ }
+ }
+ print "MADE AUTO CODE \n\n************************************************************\n\n$code\n\n************************************************************\n";
+
+ return $code;
+}
+
+
+
+
+*** TODO Make function in python that puts code into c function
+*** TODO Make function in python that generates c-function from a list of arguments
+*** TODO Resolve current issue malloc
+➜ binary_c-python git:(master) ✗ python python_API_test.py
+Traceback (most recent call last):
+ File "python_API_test.py", line 3, in <module>
+ import binary_c
+ImportError: /home/david/projects/binary_c_root/binary_c-python/libbinary_c_api.so: undefined symbol: MALLOC
+
+I get this error when I am using the master version of binary_c with either branches of the python wrapper
** General:
*** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
diff --git a/binaryc_python_utils/logging_functions.py b/binaryc_python_utils/logging_functions.py
new file mode 100644
index 0000000000000000000000000000000000000000..1d4aa71c3b6fbca3ca2222ad77ccae3c0215edac
--- /dev/null
+++ b/binaryc_python_utils/logging_functions.py
@@ -0,0 +1,105 @@
+# Functions for the automatic logging of stuff
+
+# Perl code for autogeneration
+# sub autogen_C_logging_code
+# {
+# # given a hash of arrays of variable names, where the hash
+# # key is the header, autogenerate PRINTF statements
+# my ($self) = @_;
+# my $code = undef;
+# if(defined $self->{_grid_options}->{C_auto_logging} &&
+# ref $self->{_grid_options}->{C_auto_logging} eq 'HASH'
+# )
+# {
+# $code = '';
+
+# foreach my $header (keys %{$self->{_grid_options}->{C_auto_logging}})
+# {
+# if(ref $self->{_grid_options}->{C_auto_logging}->{$header} eq 'ARRAY')
+# {
+# $code .= 'PRINTF("'.$header.' ';
+# foreach my $x (@{$self->{_grid_options}->{C_auto_logging}->{$header}})
+# {
+# $code .= '%g ';
+# }
+# $code .= '\n"';
+
+# foreach my $x (@{$self->{_grid_options}->{C_auto_logging}->{$header}})
+# {
+# $code .= ',((double)stardata->'.$x.')';
+# }
+# $code .= ');'
+# }
+# }
+# }
+# print "MADE AUTO CODE \n\n************************************************************\n\n$code\n\n************************************************************\n";
+
+# return $code;
+# }
+
+# Which is used in flexi-grid via this:
+# $population->set( C_auto_logging => {
+# 'MY_STELLAR_DATA' =>
+# [
+# 'model.time',
+# 'star[0].mass',
+# 'model.probability',
+# 'model.dt'
+# ]
+# });
+
+
+
+def autogen_C_logging_code(logging_dict):
+ """
+ Function that autogenerates PRINTF statements for binaryc
+
+ Input:
+ dictionary where the key is the header of that logging line and items which are lists of parameters that will be put in that logging line
+
+ example: {'MY_STELLAR_DATA':
+ [
+ 'model.time',
+ 'star[0].mass',
+ 'model.probability',
+ 'model.dt'
+ ']}
+ """
+
+ # Check if the input is of the correct form
+ if not type(logging_dict)==dict:
+ print("Error: please use a dictionary as input")
+
+ #
+ code = ''
+
+ # Loop over dict keys
+ for key in logging_dict:
+ print('{}'.format(key))
+
+ logging_dict_entry = logging_dict[key]
+
+ # Check if item is of correct type:
+ if type(logging_dict_entry)==list:
+ print(logging_dict_entry)
+
+ # Construct print statement
+ code += 'PRINTF("{}'.format(key)
+ code += ' {}'.format('%g '*len(logging_dict_entry))
+ code = code.strip()
+ code += '\n"'
+
+ # Add format keys
+ for param in logging_dict_entry:
+ code += ',((double)stardata->{})'.format(param)
+ code += ');'
+
+ else:
+ print('Error: please use a list for the list of parameters that you want to have logged')
+
+
+ print(repr(code))
+
+autogen_C_logging_code({'MY_STELLAR_DATA': ['model.time', 'star[0].mass'], 'my_sss2': ['model.time', 'star[1].mass']})
+
+