made first logging function

#TODO.org#

-* 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

.#TODO.org

-david@david-Lenovo-IdeaPad-S340-14IWL.21326:1572369068
\ No newline at end of file

TODO.org

 * 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?)

binaryc_python_utils/logging_functions.py

+# 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']})
+
+