dendrotweaks 0.3.1__py3-none-any.whl

dendrotweaks/membrane/io/reader.py

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+import re
+from typing import List, Dict
+import os
+
+class MODFileReader():
+    """
+    Reader class for .mod files.
+
+    Provides methods to read and preprocess .mod files.
+    Splits the content of the file into blocks for further parsing.
+
+    Attributes
+    ----------
+    content : str
+        The content of the MOD file.
+    blocks : Dict[str, List[str]]
+        The blocks of the MOD file corresponding to the
+        NMODL blocks e.g. NEURON, PARAMETER, ASSIGNED, etc.
+    unmatched : str
+        The unmatched content in the MOD file after splitting into blocks.
+    """
+
+    BLOCK_TYPES = ['TITLE',
+                  'COMMENT',
+                  'NEURON',
+                  'UNITS',
+                  'PARAMETER',
+                  'ASSIGNED',
+                  'STATE',
+                  'BREAKPOINT',
+                  'DERIVATIVE',
+                  'INITIAL',
+                  'FUNCTION',
+                  'PROCEDURE',
+                  'KINETIC']
+
+    def __init__(self):
+
+        self._original_content = None
+        self.content = None
+        self.blocks = {}
+        self.unmatched = None
+
+    # READ
+
+    def read_file(self, path_to_file: str) -> str:
+        """
+        Read the content of the file.
+
+        Parameters
+        ----------
+        path_to_file : str
+            The path to the file.
+        """
+        with open(path_to_file, 'r') as f:
+            content = f.read()
+        
+        self._file_name = os.path.basename(path_to_file).replace('.mod', '')
+        self._path_to_file = path_to_file
+        self._original_content = content
+        self.content = content
+        
+    # PREPROCESS
+
+    def preprocess(self, remove_inline_comments=True, 
+                   remove_unitsoff=True, remove_verbatim=True) -> None:
+        """
+        Preprocess the content of the file.
+        """
+        self.replace_suffix_with_name(overwirte=True)
+        if remove_inline_comments:
+            self.remove_inline_comments()
+        if remove_unitsoff:
+            self.remove_unitsoff()
+        if remove_verbatim:
+            self.remove_verbatim()
+
+    def replace_suffix_with_name(self, overwirte=False) -> None:
+        """
+        Replace the suffix in the content of the file with the file name.
+
+        Notes
+        -----
+        Suffix is a string of the form SUFFIX suffix
+
+        Parameters
+        ----------
+        overwirte : bool, optional
+            Whether to overwrite the content of the file with the modified content.
+        """
+        suffix_pattern = r'SUFFIX\s+\w+'
+        match = re.search(suffix_pattern, self.content)
+        # print(f"Replacing {match.group()} with SUFFIX {self._file_name}")
+        self.content = re.sub(suffix_pattern, f'SUFFIX {self._file_name}', self.content)
+        if overwirte:
+            self._overwrite()
+
+    def _overwrite(self) -> None:
+        """
+        Overwrite the content of the file with the modified content.
+        """
+        with open(self._path_to_file, 'w') as f:
+            f.write(self.content)
+        # print(f"Overwritten {self._path_to_file}")
+
+    def remove_inline_comments(self) -> None:
+        """
+        Remove the rest of the line after ":" from the content of the file.
+        """
+        self.content = re.sub(r':.*', '', self.content)
+        
+
+    def remove_unitsoff(self) -> None:
+        """
+        Remove 'UNITSOFF' and 'UNITSON' from the content of the file.
+        """
+        self.content = re.sub(r'UNITSOFF|UNITSON', '', self.content)
+        
+
+    def remove_verbatim(self) -> None:
+        """
+        Remove 'VERBATIM' and 'ENDVERBATIM' and everything in between from the content of the file.
+        """
+        self.content = re.sub(r'VERBATIM.*?ENDVERBATIM', '', self.content, flags=re.DOTALL)
+        
+
+    def remove_suffix_from_gbar(self) -> None:
+        """
+        Remove the suffix from 'gbar' in the content of the file.
+
+        Example
+        -------
+            gnabar -> gbar
+        """
+        self._content =  re.sub(r'\b\w*g\w*bar\w*\b', 'gbar', self._content)
+        logger.info("Removed suffix from 'gbar' (e.g. gnabar -> gbar)")
+
+    # SPLIT TO BLOCKS
+
+    def get_blocks(self, verbose=True) -> Dict[str, List[str]]:
+        """
+        Split the content of the file into blocks and return them.
+
+        Parameters
+        ----------
+        verbose : bool, optional
+            Whether to print the
+            blocks of the file.
+
+        Returns
+        -------
+        Dict[str, List[str]]
+            A dictionary of blocks where the key is the block name
+        """
+        for block_type in self.BLOCK_TYPES:
+            matches = self._get_block_regex(block_type)
+            self.blocks[block_type] = matches
+        if verbose:
+            message = f"Split content into blocks:\n"
+            message += '\n'.join([f"    {len(block_content)} - {block_name}" 
+                            for block_name, block_content in self.blocks.items()])
+            print(message)
+        self.find_unmatched_content()
+        return self.blocks
+
+    def _get_block_regex(self, block_name: str) -> List[str]:
+        """
+        Get the regex pattern for a specific block.
+
+        Example
+        -------
+            NEURON {
+                ...
+            }
+
+        Parameters:
+        ------------
+        block_name : str
+            The name of the block e.g. 'NEURON', 'PARAMETER', etc.
+
+        Returns
+        -------
+        List[str]
+            A list of matches for the block.
+        """
+        if block_name == 'TITLE':
+            pattern = r"(" + re.escape(block_name) + r"[\s\S]*?\n)"
+        elif block_name == 'COMMENT':
+            pattern = r"(" + re.escape(block_name) + r"[\s\S]*?ENDCOMMENT)"
+        else:
+            pattern = r"(\b" + re.escape(block_name) + r"\b[\s\S]*?\{(?:[^{}]*\{[^{}]*\})*[^{}]*?\})"
+        matches = re.findall(pattern, self.content, re.DOTALL)
+        return matches
+
+    def find_unmatched_content(self, verbose:bool=False) -> None:
+        """
+        Find unmatched content in the content of the file.
+
+        Parameters
+        ----------
+        verbose : bool, optional
+            Whether to print the unmatched content.
+        """
+        unmatched = self.content
+        for block_name, block in self.blocks.items():
+            for block_content in block:
+                unmatched = unmatched.replace(block_content, '')
+        unmatched = unmatched.strip()
+        if verbose:
+            if unmatched: print(f"Unmatched content:\n{unmatched}")
+            else: print("No unmatched content.")
+        self._unmatched = unmatched