Merge pull request #43 from Fluorescence-Tools/development

Improved file type inference

doc/whats_new/changes.rst

@@ -7,6 +7,7 @@ Version 0.24
 
 * Add support for sm files
 * Add support for CZ CF3 FCS files
+* Improved type tttr file type inference to mitigate crashes
 
 
 Version 0.23

ext/python/FileCheck.i

@@ -0,0 +1,6 @@
+%module tttrlib
+%{
+#include "FileCheck.h"
+%}
+
+%include "FileCheck.h"

ext/python/TTTR.py

@@ -48,19 +48,8 @@ def __init__(self, *args, **kwargs):
         import pathlib
         if isinstance(args[0], str) or isinstance(args[0], pathlib.Path):
             if len(args) == 1:
-                suffix = str(pathlib.Path(args[0]).suffix)[1:].upper()
-                obj = str(pathlib.Path(args[0]).absolute())
-                if suffix == 'HT3' or suffix == 'PTU':
-                    tttr_container_type = suffix
-                elif suffix == 'HDF' or suffix == 'H5' or suffix == 'HDF5':
-                    tttr_container_type = 'HDF'
-                else:
-                    raise ValueError(
-                        "The file type '{}' does not allow to determine "
-                        "the container format. Specify the 'tttr_container_type' "
-                        "parameter.".format(suffix)
-                    )
-                this = _tttrlib.new_TTTR(obj, tttr_container_type)
+                obj = str(pathlib.Path(args[0]).absolute().as_posix())
+                this = _tttrlib.new_TTTR(obj)
             else:
                 this = _tttrlib.new_TTTR(*args, **kwargs)
         else:

ext/python/tttrlib.i

@@ -32,6 +32,7 @@
 
 %include "info.h"
 %include "misc_types.i"
+%include "FileCheck.i"
 
 %include "TTTRHeader.i"
 %include "TTTRRange.i"

include/FileCheck.h

@@ -0,0 +1,93 @@
+#ifndef TTTRLIB_FILECHECK_H
+#define TTTRLIB_FILECHECK_H
+
+#include <iostream>
+#include <fstream>
+#include <array>
+
+#include "TTTRHeader.h"
+
+/**
+ * @brief Checks if the given file is an HDF5 file.
+ *
+ * This function opens the specified file and performs checks to determine if
+ * it conforms to the HDF5 file format.
+ *
+ * @param filename The name of the file to check.
+ * @return true if the file is an HDF5 file, false otherwise.
+ */
+bool isHDF5File(const std::string& filename);
+
+/**
+ * @brief Checks if the given file is an SM file.
+ *
+ * This function opens the specified file and reads the first 64 bits to determine
+ * if the file is an SM file, specifically checking if the value equals 2.
+ *
+ * @param filename The name of the file to check.
+ * @return true if the file is an SM file, false otherwise.
+ */
+bool isSMFile(const std::string& filename);
+
+/**
+ * @brief Checks if the given file is a PTU file.
+ *
+ * This function opens the specified file and reads the first 8 bytes (Magic) to
+ * verify if the file is a PTU file by checking if it starts with "PQTTTR".
+ *
+ * @param filename The name of the file to check.
+ * @return true if the file is a PTU file, false otherwise.
+ */
+bool isPTUFile(const std::string& filename);
+
+/**
+ * @brief Checks if the given file is an HT3 file.
+ *
+ * This function opens the specified file and reads the header to check if the
+ * file format version is "1.0", which is required for HT3 files.
+ *
+ * @param filename The name of the file to check.
+ * @return true if the file is an HT3 file, false otherwise.
+ */
+bool isHT3File(const std::string& filename);
+
+/**
+ * @brief Checks if the given file is a BH132 file.
+ *
+ * This function opens the specified file and reads the header to determine if
+ * it is a BH132 file by checking if the `macro_time_clock` is in the range (0, 10000)
+ * and if the `invalid` flag is set to true.
+ *
+ * @param filename The name of the file to check.
+ * @return true if the file is a BH132 file, false otherwise.
+ */
+bool isBH132File(const std::string& filename);
+
+
+/**
+ * @brief Determines the type of the TTTR file based on its content.
+ *
+ * This function uses various type-checking functions to infer the type of the
+ * given TTTR file. It performs checks in a specific order to identify the file type.
+ * Returns a container identifier corresponding to the file type.
+ *
+ * @param fn The name of the file to check.
+ * @return An integer representing the type of the TTTR file, or -1 if the type cannot be determined.
+ */
+int inferTTTRFileType(const char* fn);
+
+
+/**
+ * @brief Determines if the given file is a Carl Zeiss Confocor3 (CZ Confocor3) raw data file.
+ *
+ * This function reads the header of the file and checks for specific patterns
+ * to determine if the file is of type CZ Confocor3. It performs the necessary checks
+ * and returns true if the file type is identified, otherwise false.
+ *
+ * @param filename The name of the file to check.
+ * @return True if the file is a CZ Confocor3 file, false otherwise.
+ */
+bool isCZConfocor3File(const std::string& filename);
+
+
+#endif //TTTRLIB_FILECHECK_H

include/TTTR.h

@@ -27,6 +27,7 @@
 
 #include "Histogram.h"
 #include "TTTRHeader.h"
+#include "FileCheck.h"
 #include "TTTRMask.h"
 #include "TTTRRecordReader.h"
 #include "TTTRRecordTypes.h"
@@ -683,6 +684,25 @@ class TTTR : public std::enable_shared_from_this<TTTR>{
     */
     TTTR(const char *filename, int container_type, bool read_input);
 
+    /**
+     * @brief Constructs a TTTR object based on the provided filename by inferring the file type.
+     *
+     * This constructor initializes a TTTR object by automatically determining the file type
+     * from the given filename. It utilizes the `inferTTTRFileType` function to identify
+     * the type of TTTR file and then calls the existing constructor with the inferred container type.
+     * The internal state related to the container type is initialized based on the file type inference.
+     *
+     * The constructor performs the following actions:
+     * - Infers the container type from the filename using `inferTTTRFileType`.
+     * - Initializes the TTTR object using the existing constructor `TTTR(const char *fn, int container_type, bool some_flag)`.
+     * - Sets the container type string based on the inferred container type.
+     * - Handles cases where the inferred container type is not supported by setting the container type string to `"Unknown"`
+     *   and logging an error message.
+     *
+     * @param filename The path to the TTTR file to be analyzed. The file type is inferred based on this filename.
+     */
+    TTTR(const char *filename);
+
     /*!
      * Constructor for TTTR object that reads the content of the file.
      *