Added function for reading a catalog

Reviewed-on: episodes-platform/shared-snippets#2
Reviewed-by: asia <asia@noreply.example.org>

matlab/logging/base_logger.m

@@ -10,6 +10,9 @@
 % It follows the Singleton pattern to ensure that only one instance of the logger
 % exists throughout the application.
 %
+% The log file is specified by the environment variable 'APP_LOG_FILE'. If
+% the variable is not set, a default file 'base-logger-log.log' is used.
+%
 % Properties:
 %   fid - (private) The file identifier for the log file. This is used to write logs.
 %
@@ -17,20 +20,20 @@
 %
 %   getInstance() - Retrieves the singleton instance of the logger.
 %
-%   trace(message) - Logs a message with TRACE level.
+%   trace(varargin) - Logs one or more messages with TRACE level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   debug(message) - Logs a message with DEBUG level.
+%   debug(varargin) - Logs one or more messages with DEBUG level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   info(message) - Logs a message with INFO level.
+%   info(varargin) - Logs one or more messages with INFO level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   warning(message) - Logs a message with WARNING level.
+%   warning(varargin) - Logs one or more messages with WARNING level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   error(message) - Logs a message with ERROR level.
+%   error(varargin) - Logs one or more messages with ERROR level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
 %   delete() - Destructor method that closes the file identifier when the logger is deleted.
 %
@@ -63,7 +66,11 @@ classdef base_logger < handle
 
     methods(Access=private)
         function this = base_logger()
-            this.fid = fopen(getenv("APP_LOG_FILE"), 'a');
+            logFileName = getenv("APP_LOG_FILE");
+            if isempty(logFileName)
+                logFileName = 'base-logger-log.log';
+            end
+            this.fid = fopen(logFileName, 'a');
             if this.fid == -1
                 error('Failed to open log file');
             end

octave/logging/base_logger.m

@@ -10,6 +10,9 @@
 % It follows the Singleton pattern to ensure that only one instance of the logger
 % exists throughout the application.
 %
+% The log file is specified by the environment variable 'APP_LOG_FILE'. If
+% the variable is not set, a default file 'base-logger-log.log' is used.
+%
 % Properties:
 %   fid - (private) The file identifier for the log file. This is used to write logs.
 %
@@ -17,20 +20,20 @@
 %
 %   getInstance() - Retrieves the singleton instance of the logger.
 %
-%   trace(message) - Logs a message with TRACE level.
+%   trace(varargin) - Logs one or more messages with TRACE level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   debug(message) - Logs a message with DEBUG level.
+%   debug(varargin) - Logs one or more messages with DEBUG level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   info(message) - Logs a message with INFO level.
+%   info(varargin) - Logs one or more messages with INFO level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   warning(message) - Logs a message with WARNING level.
+%   warning(varargin) - Logs one or more messages with WARNING level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
-%   error(message) - Logs a message with ERROR level.
+%   error(varargin) - Logs one or more messages with ERROR level.
-%     @param message The message to log.
+%     @param varargin The messages to log. Can be strings, numbers, or MException objects.
 %
 %   delete() - Destructor method that closes the file identifier when the logger is deleted.
 %
@@ -63,7 +66,11 @@ classdef base_logger < handle
 
     methods
         function this = base_logger()
-            this.fid = fopen(getenv("APP_LOG_FILE"), 'a');
+            logFileName = getenv("APP_LOG_FILE");
+            if isempty(logFileName)
+                logFileName = 'base-logger-log.log';
+            end
+            this.fid = fopen(logFileName, 'a');
             if this.fid == -1
                 error('Failed to open log file');
             end

python/catalog/find_catalog_column.py

@@ -0,0 +1,36 @@
+# -----------------
+# Copyright © 2024 ACK Cyfronet AGH, Poland.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# This work was partially funded by DT-GEO Project.
+# -----------------
+def find_catalog_column(catalog, field_name):
+    """
+    Finds the index of a column in the catalog based on its field name.
+
+    Parameters:
+        catalog (np.ndarray): A structured NumPy array representing a catalog in EPISODES Platform format:
+                              https://docs.cyfronet.pl/display/ISDOC/Catalogs
+        field_name (str): The field name of the entry to search for.
+
+    Returns:
+        int: The index of the entry matching the given field name.
+
+    Raises:
+        ValueError: If the specified field name is not found in the catalog.
+    """
+    for idx, col in enumerate(catalog):
+        if col['field'] == field_name:
+            return idx
+    raise ValueError(f'No {field_name} field found in the catalog.')

python/catalog/read_catalog.py

@@ -0,0 +1,22 @@
+# -----------------
+# Copyright © 2025 ACK Cyfronet AGH, Poland.
+# -----------------
+from scipy.io import loadmat, whosmat
+  
+def read_catalog(catalog_path):
+    """
+    Reads the provided catalog in EPISODES Platform format (https://docs.cyfronet.pl/display/ISDOC/Catalogs)
+
+    Parameters:
+        catalog_path: Path to the catalog file to be read.
+
+    Returns:
+        catalog (np.ndarray): A structured NumPy array representing the catalog.
+
+    Raises:
+        ValueError: If the specified field name is not found in the catalog.
+    """
+    catalog_contents = loadmat(catalog_path, mat_dtype=True)
+    catalog_field_name = whosmat(catalog_path)[0][0] # Getting the name of first non-metadata field
+    catalog = catalog_contents[catalog_field_name][0]
+    return catalog

python/catalog/sort_by_time.py

@@ -0,0 +1,44 @@
+# -----------------
+# Copyright © 2024 ACK Cyfronet AGH, Poland.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# This work was partially funded by DT-GEO Project.
+# -----------------
+import numpy as np
+from find_catalog_column import find_catalog_column
+
+def sort_by_time(catalog):
+    """
+    Sorts the given catalog based on the 'Time' column. Requires find_catalog_column script to work.
+
+    Parameters:
+        catalog (np.ndarray): A structured NumPy array representing a seismic catalog in EPISODES Platform format:
+                              https://docs.cyfronet.pl/display/ISDOC/Seismic+catalog
+
+    Returns:
+        np.ndarray: The sorted catalog, where rows in 'val' fields are ordered by ascending 'Time' values.
+
+    Raises:
+        ValueError: If the 'Time' column is not found in the catalog.
+    """
+    time_col_index = find_catalog_column(catalog, 'Time')
+
+    time_values = catalog[time_col_index]['val'].flatten()
+    sorted_indexes = np.argsort(time_values)
+
+    sorted_catalog = catalog.copy()
+    for field in sorted_catalog:
+        field['val'] = field['val'][sorted_indexes]
+
+    return sorted_catalog

python/logging/base_logger.py

@@ -11,8 +11,10 @@ def getDefaultLogger(name):
     Retrieves or creates a logger with the specified name and sets it up with a file handler.
     
     The logger is configured to write log messages to the file path specified by the
-    'DEFAULT_LOG_PATH' environment variable. It uses the 'INFO' level as the default
+    'APP_LOG_FILE' environment variable. If the environment variable is not set,
-    logging level and writes log entries in the following format:
+    the logger will write to the file 'base-logger-log.log' in the current
+    working directory. The logger uses the 'INFO' level as the default logging level
+    and writes log entries in the following format:
     
     'YYYY-MM-DD HH:MM:SS,ms LEVEL logger_name message'
     
@@ -30,13 +32,9 @@ def getDefaultLogger(name):
     --------
     logger : logging.Logger
         A logger instance with the specified name. The logger is configured with a 
-        file handler that writes to the file specified by the 'DEFAULT_LOG_PATH' 
+        file handler that writes to the file specified by the 'APP_LOG_FILE' 
-        environment variable.
+        environment variable, or to 'base-logger-log.log' if the environment 
-    
+        variable is not set.
-    Raises:
-    -------
-    KeyError:
-        If the 'DEFAULT_LOG_PATH' environment variable is not set.
     
     Example:
     --------
@@ -47,10 +45,15 @@ def getDefaultLogger(name):
     except Exception:
         logger.exception('An error occurred')
 
+    Notes:
+    ------
+    - The 'APP_LOG_FILE' environment variable should specify the full path to the log file.
+    - If 'APP_LOG_FILE' is not set, logs will be written to 'base-logger-log.log'.
+
     """
     logger = logging.getLogger(name)
     if not logger.hasHandlers():
-        file_handler = logging.FileHandler(os.environ['APP_LOG_FILE'], mode='a')
+        file_handler = logging.FileHandler(os.environ.get('APP_LOG_FILE', 'base-logger-log.log'), mode='a')
         formatter = logging.Formatter('%(asctime)s,%(msecs)d %(levelname)s %(name)s %(message)s')
         file_handler.setFormatter(formatter)
         logger.addHandler(file_handler)