dev(meta):new class to read .pid file and some code cleanup

Author: grololo06

src/ZooProcess_lib/Converter.py

@@ -9,7 +9,8 @@
 
 from .ImageJLike import convert_16bit_image_to_8bit_min_max
 from .Legacy import averaged_median_mean
-from .img_tools import rotate90c, Lut, minAndMax, saveimage, load_tiff_image_and_info
+from .img_tools import rotate90c, minAndMax, saveimage, load_tiff_image_and_info
+from .LegacyMeta import LutFile
 
 CV2_VERTICAL_FLIP_CODE = 0
 CV2_NO_TIFF_COMPRESSION = 1
@@ -20,7 +21,7 @@ class Converter(object):
     In charge of images 16->8 bits conversion
     """
 
-    def __init__(self, lut: Lut):
+    def __init__(self, lut: LutFile):
         self.lut = lut
 
     def do_file_to_file(self, from_file: Path, to_file: Path):

src/ZooProcess_lib/Extractor.py

@@ -68,14 +68,10 @@ def extract_all_to_images(
 
     def _add_border_and_legend(self, image: np.ndarray, longline: float):
         height, width = image.shape
-        # Resized image is plain one...
-        # ...+ 20% border and footer in height
-        final_height = round(height * 1.4 + self.FOOTER)
-        # ...and +20% border with enough space for line in width
-        final_width = round(max(width * 1.4, longline + 2 * self.X1))
+        final_height, final_width = self.get_final_dimensions(height, width, longline)
         # draw a new frame big enough and paste
         resized = np.full((final_height, final_width), 255, dtype=np.uint8)
-        y_offset = (final_height - self.FOOTER - height) // 2
+        y_offset = (final_height - Extractor.FOOTER - height) // 2
         x_offset = (final_width - width) // 2
         resized[y_offset : y_offset + height, x_offset : x_offset + width] = image
         # Paint the scale
@@ -114,6 +110,15 @@ def _add_border_and_legend(self, image: np.ndarray, longline: float):
         # print(f"height: {height}, width: {width} => {final_height}x{final_width} px xoffset: {x_offset} yoffset: {y_offset}")
         return resized
 
+    @staticmethod
+    def get_final_dimensions(height: int, width: int, longline: float):
+        # Resized image is plain one...
+        # ...+ 20% border and footer in height
+        final_height = round(height * 1.4 + Extractor.FOOTER)
+        # ...and +20% border with enough space for line in width
+        final_width = round(max(width * 1.4, longline + 2 * Extractor.X1))
+        return final_height, final_width
+
     def extract_image_at_ROI(
         self, image: np.ndarray, a_roi: ROI, erasing_background: bool = False
     ) -> np.ndarray:

src/ZooProcess_lib/LegacyConfig.py

@@ -1,50 +1,9 @@
-# A .lut file contains processing directives for a whole project
 import dataclasses
 from configparser import ConfigParser
 
 from pathlib import Path
 
 
-class Lut:
-    def __init__(self):
-        self.min: int = 0
-        self.max: int = 65536
-        self.gamma: float = 1
-        self.sens: str = "before"
-        # Appeared in a later version
-        self.adjust: str = "no"
-        self.odrange: float = 1.8
-        # Appeared in a later version
-        self.ratio: float = 1.15
-        # Appeared in a later version
-        self.sizelimit: int = 800  # Unused?
-        self.overlap: float = 0.07
-        # Appeared in a later version
-        self.medianchoice: str = "no"
-        self.medianvalue: int = 1
-        # Appeared in a later version
-        self.resolutionreduct: int = 1200
-
-    @staticmethod
-    def read(path: Path) -> "Lut":
-        ret = Lut()
-        with open(path, "r") as f:
-            lines = f.readlines()
-            for a_var_name, a_line in zip(ret.__dict__.keys(), lines):
-                a_var = getattr(ret, a_var_name)
-                # Below for clarity and extensibility, as we could use directly the class, class(a_line)
-                if isinstance(a_var, int):
-                    setattr(ret, a_var_name, int(a_line))
-                elif isinstance(a_var, float):
-                    setattr(ret, a_var_name, float(a_line))
-                elif isinstance(a_var, str):
-                    setattr(ret, a_var_name, a_line.strip())
-        # From legacy macro, there is a typo "od_g_range" so the code doesn't do what it should I guess
-        # if ret.odrange >= 3:
-        #     ret.odgrange = 1.15
-        return ret
-
-
 # Full dump of a config file, for future use:
 # _Used_:
 # background_process= last
@@ -114,135 +73,3 @@ def read(cls, path: Path) -> "ZooscanConfig":
                         raise
                 args.append(value)
             return ZooscanConfig(*args)
-
-
-@dataclasses.dataclass(frozen=False)
-class ProjectMeta:
-    """
-    Class to read and store metadata from a metadata.txt file.
-    All fields are explicitly defined with proper type annotations.
-    """
-
-    # String fields
-    SampleId: str = ""  # e.g. apero2023_tha_bioness_sup2000_017_st66_d_n1
-    Scanop: str = ""  # e.g. adelaide_perruchon
-    Ship: str = ""  # e.g. thalassa
-    Scientificprog: str = ""  # e.g. apero
-    Date: str = ""  # e.g. 20230704-0503
-    CTDref: str = ""  # e.g. apero_bio_ctd_017
-    Otherref: str = ""  # e.g. apero_bio_uvp6_017u
-    Nettype: str = ""  # e.g. bioness
-    Observation: str = ""  # e.g. no
-    SubMethod: str = ""  # e.g. motoda
-    Sample_comment: str = ""  # e.g. vol_zooprocess_saisi
-    barcode: str = ""  # e.g. ape000000147
-    FracId: str = ""  # e.g. d2_4_sur_4
-
-    # Integer fields
-    StationId: int = -1  # e.g. 66
-    Townb: int = -1  # e.g. 1
-    Towtype: int = -1  # e.g. 1
-    Netmesh: int = -1  # e.g. 2000
-    Netsurf: int = -1  # e.g. 1
-    Vol: int = -1  # e.g. 357
-    Fracmin: int = -1  # e.g. 2000
-    Fracsup: int = -1  # e.g. 999999
-    Fracnb: int = -1  # e.g. 4
-    Code: int = -1  # e.g. 1
-    CellPart: int = -1  # e.g. 1
-    Replicates: int = -1  # e.g. 1
-    VolIni: int = -1  # e.g. 1
-    VolPrec: int = -1  # e.g. 1
-    vol_qc: int = -1  # e.g. 1
-    depth_qc: int = -1  # e.g. 1
-    sample_qc: int = -1  # e.g. 1111
-
-    # Float fields
-    Depth: float = -1.0  # e.g. 99999
-    Zmax: float = -1.0  # e.g. 1008
-    Zmin: float = -1.0  # e.g. 820
-    net_duration: float = -1.0  # e.g. 20
-    ship_speed_knots: float = -1.0  # e.g. 2
-    cable_length: float = -1.0  # e.g. 9999
-    cable_angle: float = -1.0  # e.g. 99999
-    cable_speed: float = -1.0  # e.g. 0
-    nb_jar: float = -1.0  # e.g. 1
-    Latitude: float = -1.0  # e.g. 51.4322000
-    Longitude: float = -1.0  # e.g. 18.3108000
-    latitude_end: float = -1.0  # e.g. 51.4421000
-    longitude_end: float = -1.0  # e.g. 18.3417000
-
-    @classmethod
-    def read(cls, path: Path) -> "ProjectMeta":
-        """
-        Read a metadata.txt file and return a ProjectMeta instance with fields
-        populated from the file.
-        """
-        meta = ProjectMeta()
-        with open(path, "r") as strm:
-            for line in strm:
-                if "=" in line:
-                    key, value = line.split("=", 1)
-                    key = key.strip()
-                    value = value.strip()
-
-                    if hasattr(meta, key):
-                        field_type = type(getattr(meta, key))
-                        try:
-                            if field_type == int:
-                                setattr(meta, key, int(value))
-                            elif field_type == float:
-                                setattr(meta, key, float(value))
-                            else:
-                                setattr(meta, key, value)
-                        except ValueError:
-                            # If conversion fails, keep as string
-                            setattr(meta, key, value)
-                    else:
-                        # For any fields not explicitly defined, add them as strings
-                        setattr(meta, key, value)
-
-        return meta
-
-    def _relevant_attributes(self):
-        """
-        Generator that yields relevant attributes for writing to a metadata file.
-        Yields tuples of (attr_name, attr_value) for non-default attributes.
-        """
-        for attr_name in dir(self):
-            # Skip special attributes, methods, and class variables
-            if (
-                attr_name.startswith("__")
-                or callable(getattr(self, attr_name))
-                or attr_name == "__annotations__"
-            ):
-                continue
-
-            # Get the attribute value
-            attr_value = getattr(self, attr_name)
-
-            # Skip default values for primitive types
-            if attr_value == "" or attr_value == -1 or attr_value == -1.0:
-                continue
-
-            yield attr_name, attr_value
-
-    def to_dict(self) -> dict:
-        """
-        Convert the ProjectMeta instance to a dictionary using the _relevant_attributes generator.
-        Returns a dictionary with attribute names as keys and their values as values.
-        """
-        return {
-            attr_name: attr_value
-            for attr_name, attr_value in self._relevant_attributes()
-        }
-
-    def write(self, path: Path) -> None:
-        """
-        Write the ProjectMeta instance to a metadata.txt file in the same format
-        as it is read.
-        """
-        with open(path, "w") as strm:
-            # Write all relevant attributes to the file
-            for attr_name, attr_value in self._relevant_attributes():
-                strm.write(f"{attr_name}= {attr_value}\n")