Add intial version of refinement function

nafuma/xrd/refinement.py

@@ -1,17 +1,22 @@
+from email.policy import default
 import os
 import shutil
-import time
+import subprocess
 import re
+
+import time
 import datetime
+
 import warnings
 
 import nafuma.auxillary as aux
 
+
 def make_big_inp(data: dict, options={}):
     ''' Generates a big .INP-file with all filenames found in data["path"]. Uses a template .INP-file (which has to be generated manually from an initial refinement in TOPAS) and appends this to a large .INP-file
     while changing the filenames. '''
 
-    required_options = ['template', 'output', 'overwrite', 'backup', 'backup_dir', 'include', 'topas_options', 'save_dir', 'log', 'logfile']
+    required_options = ['template', 'output', 'overwrite', 'backup', 'backup_dir', 'include', 'topas_options', 'save_results', 'save_dir', 'log', 'logfile']
 
     default_options = {
         'template': 'start.inp', # Name of the template .INP-file
@@ -20,7 +25,19 @@ def make_big_inp(data: dict, options={}):
         'backup': True, # Toggles backup on / off. Makes a backup of the file if it already exists. Only runs if overwrite is enabled.
         'backup_dir': 'backup', # Specifies the path where the backup files should be located
         'include': [],
-        'topas_options': {
+        'topas_options': None,
+        'save_results': True,
+        'save_dir': 'results',
+        'log': False,
+        'logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_generate_big_inp.log',
+    }
+
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+    required_topas_options = ['iters', 'chi2_convergence_criteria', 'bootstrap_errors', 'A_matrix_memory_allowed_in_Mbytes', 'approximate_A', 'conserve_memory', 'do_errors', 'continue_after_convergence', 'num_runs']
+    default_topas_options = {
+            'iters': 100000,
+            'chi2_convergence_criteria': 0.001,
             'bootstrap_errors': None,
             'A_matrix_memory_allowed_in_Mbytes': None,
             'approximate_A': False,
@@ -28,13 +45,9 @@ def make_big_inp(data: dict, options={}):
             'do_errors': False,
             'continue_after_convergence': False,
             'num_runs': None,
-        },
-        'save_dir': 'results',
-        'log': False,
-        'logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_generate_big_inp.log',
         }
 
-    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+    options['topas_options'] = aux.update_options(options=options['topas_options'], required_options=required_topas_options, default_options=default_topas_options)
 
 
     if not os.path.exists(options['template']):
@@ -55,45 +68,101 @@ def make_big_inp(data: dict, options={}):
         aux.backup_file(filename=options['output'], backup_dir=options['backup_dir'])
 
 
-
     runlist = os.path.join(os.path.dirname(options['output']), 'runlist.txt')
     options['include'].append(runlist)
 
     with open(options['template'], 'r') as template, open(options['output'], 'w', newline='\n') as output, open(runlist, 'w', newline='\n') as runlist:
     
         write_headers(output, options)
+
         template = template.read()
         
         for i, path in enumerate(data['path']):
 
-            s = change_labels_and_paths(template, path, i, options)
+            s = make_inp_entry(template=template, xdd=path, num=i, options=options)
             output.write(s)
+            output.write('\n\n')
             
             runlist.write('#define \tUSE_'+f'{i}'.zfill(4) + '\n')
 
 
 
 def write_headers(fout, options):
+    # FIXME Could modify this to make sure that certain combinations of options is not written, such as both do_errors and bootstrap_errors. 
 
     for file in options['include']:
         fout.write(f'#include {file} \n')
 
     fout.write('\n')
 
+    if options['save_results']:
+        fout.write('#define output \n')
+    
+    fout.write('\n')
+
     for option, value in options['topas_options'].items():
         if value:
+            if isinstance(value, bool):
+                fout.write(f'{option} \n')
+            else:
                 fout.write(f'{option} {value} \n')
 
 
+def get_headers(inp):
 
-def change_labels_and_paths(template, path, i, options):
+    with open(inp, 'r') as inp:
+        headers = []
+
+        line = inp.readline()
+
+        while not all(keyword in line for keyword in ['out', 'append']):
+            line = inp.readline()
+
+        # Jump down to lines
+        line = inp.readline()
+        line = inp.readline()
+
+        while not 'Out_String' in line:
+                
+            if line.split():
+                header = line.split()[1]
+                if all(keyword in header for keyword in ['Get', '(', ')']):
+                    header = header[4:-1]
+
+                headers.append(header)
+
+            line = inp.readline()
+
+
+    return headers
+            
+
+def get_paths(inp):
+
+    paths = []
+
+    with open(inp, 'r') as inp:
+        lines = inp.readlines()
+
+    for line in lines:
+        if all(keyword in line for keyword in ['out', 'append']):
+            paths.append(line.split()[1])
+
+
+    return paths
+
+def make_inp_entry(template: str, xdd: str, num: int, options: dict) -> str:
+    ''' Takes a template and creates an entry with xdd as path to file and with number num.'''
 
     temp_xdd = find_xdd_in_inp(options['template'])
 
-    # Replace diffractogram-path
-    s = template.replace(temp_xdd, path).replace('XXXX', f'{i}'.zfill(4))
 
-    basename = os.path.basename(path).split(".")[0]
+    num_str = f'{num}'.zfill(4)
+    
+    # Replace diffractogram-path
+    s = template.replace(temp_xdd, xdd).replace('XXXX', num_str)
+
+    basename = os.path.basename(xdd).split(".")[0]
     
     # Define regular expressions for output lines
     regs = [r'Out_Riet\([\S]*\)',
@@ -106,23 +175,24 @@ def change_labels_and_paths(template, path, i, options):
     
     # Define substitute strings for output lines
     subs = [f'Out_Riet({options["save_dir"]}/{basename}_riet.xy)',
-            f'Out_CIF_STR({options["save_dir"]}/{basename}.cif))',
+            f'Out_CIF_STR({options["save_dir"]}/{basename}.cif)',
-            f'Out_CIF_ADPs({options["save_dir"]}/{basename}.cif))',
+            f'Out_CIF_ADPs({options["save_dir"]}/{basename}.cif)',
-            f'Out_CIF_Bonds_Angles({options["save_dir"]}/{basename}.cif))',
+            f'Out_CIF_Bonds_Angles({options["save_dir"]}/{basename}.cif)',
             f'Out_FCF({options["save_dir"]}/{basename}.fcf)',
             f'Create_hklm_d_Th2_Ip_file({options["save_dir"]}/{basename}_hkl.dat)',
-            f'out \t {options["save_dir"]}/{basename}_refined_params.dat']
+            f'out \t {options["save_dir"]}/{basename}_refined_params.dat \t append']
 
     # Substitute strings in output lines
     for reg, sub in zip(regs, subs):
         s = re.sub(reg, sub, s)
 
 
+
     return s
 
 
 
-def find_xdd_in_inp(path):
+def find_xdd_in_inp(path: str) -> str:
     ''' Finds the path to the .xy / .xye scan in a given .INP-file. Assumes only one occurence of xdd and will return the last one no matter what, but outputs a UserWarning if more than one xdd is found.'''
 
     with open(path, 'r') as f:
@@ -139,3 +209,67 @@ def find_xdd_in_inp(path):
         warnings.warn(f'More than one path was found in {path}. Returning last occurence - please make sure this is what you want!')
 
     return xdd
+
+
+def refine(data: dict, options={}):
+    ''' Calls TOPAS from options['topas_path'], which should point to tc.exe in the TOPAS-folder. If not explicitly passed, will try to use what is in topas.conf.'''
+
+    required_options = ['topas_path', 'topas_log', 'topas_logfile', 'log', 'logfile', 'overwrite']
+
+    default_options = {
+        'topas_path': None,
+        'topas_log': False,
+        'topas_logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_topas.out',
+        'log': False,
+        'logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_generate_big_inp.log',
+        'overwrite': False
+    }
+
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+    if not options['topas_path']:
+        import nafuma.xrd as xrd
+
+        # Open topas.conf in the nafuma/xrd 
+        with open(os.path.join(os.path.dirname(xrd.__file__), 'topas.conf'), 'r') as f:
+            topas_base = f.read()
+
+        options['topas_path'] = os.path.join(topas_base, 'tc.exe')
+
+
+    # Check to see if the executable exists
+    if not os.path.exists(options['topas_path']):
+        raise Exception('TOPAS executable not found! Please explicitly pass path to tc.exe directly in options["topas_path"] or change base folder in topas.conf to the correct one.')
+
+
+    # Create folders if they don't exist
+    paths, headers = get_paths(data['inp']), get_headers(data['inp'])
+    
+    for path in paths:
+        dirname = os.path.dirname(path)
+
+        if dirname and not os.path.isdir(dirname):
+            os.makedirs(dirname)
+
+        if not os.path.exists(path) or options['overwrite']:
+            with open(path, 'w') as results:
+                for header in headers:
+                    results.write(header+'\t')
+
+                results.write('\n')
+        else:
+            raise Exception(f'Results file already exists: {path}')
+
+
+    # Create shell command
+    command = ' '.join([options['topas_path'], data['inp']])
+
+    # Append output if logging is enabled
+    if options['topas_log']:
+        command = ' '.join([command, f'>{options["topas_logfile"]}'])
+
+        if os.path.dirname(options['topas_logfile']) and not os.path.isdir(os.path.dirname(options['topas_logfile'])):
+            os.makedirs(os.path.dirname(options['topas_logfile']))
+
+    
+    subprocess.call(command, shell=True)

nafuma/xrd/topas.conf

@@ -0,0 +1 @@
+C:/TOPAS6/