removed symlinks to support windows

.gitignore

@@ -228,3 +228,8 @@ test*
 
 processing_results*
 plots*
+
+# Runtime state files - managed by application
+vna_system/binary_input/current_input.json
+vna_system/calibration/current_calibration.json
+vna_system/references/current_reference.json

vna_system/binary_input/current_input.bin

@@ -1 +0,0 @@
-config_inputs/s11_start100_stop8800_points1000_bw1khz.bin

vna_system/calibration/current_calibration

@@ -1 +0,0 @@
-s11_start100_stop8800_points1000_bw1khz/вфыввф

vna_system/core/acquisition/data_acquisition.py

@@ -1,8 +1,10 @@
 import io
+import json
 import os
 import struct
 import threading
 import time
+from pathlib import Path
 from typing import BinaryIO
 
 import serial
@@ -20,7 +22,8 @@ class VNADataAcquisition:
 
     def __init__(self) -> None:
         # Configuration
-        self.bin_log_path: str = cfg.BIN_INPUT_FILE_PATH
+        self.current_input_json = Path(cfg.BASE_DIR) / "binary_input" / "current_input.json"
+        self.config_inputs_dir = Path(cfg.BASE_DIR) / "binary_input" / "config_inputs"
         self.baud: int = cfg.DEFAULT_BAUD_RATE
 
         # Dependencies
@@ -42,7 +45,32 @@ class VNADataAcquisition:
         self._collected_rx_payloads: list[bytes] = []
         self._meas_cmds_in_sweep: int = 0
 
-        logger.debug("VNADataAcquisition initialized", baud=self.baud, bin_log_path=self.bin_log_path)
+        logger.debug("VNADataAcquisition initialized", baud=self.baud)
+
+    def _get_current_bin_path(self) -> Path | None:
+        """Get the path to the current binary input file from JSON config."""
+        if not self.current_input_json.exists():
+            logger.warning("Current input JSON not found", path=str(self.current_input_json))
+            return None
+
+        try:
+            with self.current_input_json.open("r", encoding="utf-8") as f:
+                current_info = json.load(f)
+
+            filename = current_info.get("filename")
+            if not filename:
+                logger.warning("Invalid current input JSON format")
+                return None
+
+            bin_path = self.config_inputs_dir / filename
+            if not bin_path.exists():
+                logger.warning("Current input binary file not found", path=str(bin_path))
+                return None
+
+            return bin_path
+        except Exception as exc:  # noqa: BLE001
+            logger.error("Failed to load current input config", error=repr(exc))
+            return None
 
     # --------------------------------------------------------------------- #
     # Lifecycle
@@ -165,12 +193,19 @@ class VNADataAcquisition:
 
                 logger.debug("Using port", device=port, baud=self.baud)
 
+                # Get current binary input file path
+                bin_path = self._get_current_bin_path()
+                if not bin_path:
+                    logger.error("No current binary input configured, waiting...")
+                    time.sleep(1.0)
+                    continue
+
                 # Open serial + process one sweep from the binary log
                 with serial.Serial(port, self.baud) as ser:
                     self._drain_serial_input(ser)
 
                     # Open the log file each iteration to read the next sweep from start
-                    with open(self.bin_log_path, "rb") as raw:
+                    with open(bin_path, "rb") as raw:
                         buffered = io.BufferedReader(raw, buffer_size=cfg.SERIAL_BUFFER_SIZE)
                         self._process_sweep_data(buffered, ser)
 

vna_system/core/config.py

@@ -47,10 +47,6 @@ EXPECTED_POINTS_PER_SWEEP = 1000
 SWEEP_BUFFER_MAX_SIZE = 100  # Maximum number of sweeps to store in circular buffer
 SERIAL_BUFFER_SIZE = 512 * 1024
 
-# -----------------------------------------------------------------------------
-# Log file settings (binary input path, not to be confused with text logs)
-# -----------------------------------------------------------------------------
-BIN_INPUT_FILE_PATH = "./vna_system/binary_input/current_input.bin"  # Symlink to current binary input
 
 # -----------------------------------------------------------------------------
 # Binary log format constants

vna_system/core/processors/configs/bscan_config.json

@@ -1,5 +1,5 @@
 {
-  "open_air": false,
+  "open_air": true,
   "axis": "real",
   "data_limitation": "ph_only_1",
   "cut": 0.816,

vna_system/core/processors/configs/magnitude_config.json

@@ -1,5 +1,5 @@
 {
   "y_min": -80,
   "y_max": 40,
-  "show_phase": false
+  "show_phase": true
 }

vna_system/core/settings/calibration_manager.py

@@ -86,7 +86,7 @@ class CalibrationManager:
     Layout
     ------
     <BASE_DIR>/calibration/
-        ├─ current_calibration -> <preset_dir>/<calibration_name>
+        ├─ current_calibration.json  # Current active calibration metadata
         ├─ <preset_name>/
         │    └─ <calibration_name>/
         │         ├─ open.json / short.json / load.json / through.json
@@ -97,7 +97,7 @@ class CalibrationManager:
     def __init__(self, base_dir: Path | None = None) -> None:
         self.base_dir = Path(base_dir or cfg.BASE_DIR)
         self.calibration_dir = self.base_dir / "calibration"
-        self.current_calibration_symlink = self.calibration_dir / "current_calibration"
+        self.current_calibration_file = self.calibration_dir / "current_calibration.json"
         self.calibration_dir.mkdir(parents=True, exist_ok=True)
 
         self._current_working_set: CalibrationSet | None = None
@@ -268,10 +268,10 @@ class CalibrationManager:
         }
 
     # ------------------------------------------------------------------ #
-    # Current calibration (symlink)
+    # Current calibration (JSON file)
     # ------------------------------------------------------------------ #
     def set_current_calibration(self, preset: ConfigPreset, calibration_name: str) -> None:
-        """Point the `current_calibration` symlink to the chosen calibration dir."""
+        """Save the current calibration selection to JSON file."""
         preset_dir = self._get_preset_calibration_dir(preset)
         calib_dir = preset_dir / calibration_name
         if not calib_dir.exists():
@@ -281,60 +281,59 @@ class CalibrationManager:
         if not info.get("is_complete", False):
             raise ValueError(f"Calibration {calibration_name} is incomplete")
 
-        # Refresh symlink
+        # Write current calibration info to JSON file
         try:
-            if self.current_calibration_symlink.exists() or self.current_calibration_symlink.is_symlink():
+            current_info = {
-                self.current_calibration_symlink.unlink()
+                "preset_filename": preset.filename,
-        except Exception as exc:  # noqa: BLE001
+                "calibration_name": calibration_name,
-            logger.warning("Failed to remove existing current_calibration link", error=repr(exc))
+                "preset_dir": preset.filename.replace(".bin", ""),
-
+                "updated_at": datetime.now().isoformat()
-        try:
+            }
-            # Create a relative link when possible to keep the tree portable
+            self._atomic_json_write(self.current_calibration_file, current_info)
-            relative = calib_dir
-            try:
-                relative = calib_dir.relative_to(self.calibration_dir)
-            except ValueError:
-                pass
-            self.current_calibration_symlink.symlink_to(relative)
             logger.info("Current calibration set", preset=preset.filename, name=calibration_name)
         except Exception as exc:  # noqa: BLE001
-            logger.error("Failed to create current_calibration symlink", error=repr(exc))
+            logger.error("Failed to set current calibration", error=repr(exc))
             raise
 
     def get_current_calibration(self, current_preset: ConfigPreset) -> CalibrationSet | None:
         """
-        Resolve and load the calibration currently pointed to by the symlink.
+        Load the calibration currently saved in JSON file.
 
-        Returns None if the link doesn't exist, points to an invalid location,
+        Returns None if the file doesn't exist, is invalid,
         or targets a different preset.
         """
-        if not self.current_calibration_symlink.exists():
+        if not self.current_calibration_file.exists():
             return None
 
         try:
-            target = self.current_calibration_symlink.resolve()
+            with self.current_calibration_file.open("r", encoding="utf-8") as f:
-            calibration_name = target.name
+                current_info = json.load(f)
-            preset_dir_name = target.parent.name  # <preset_name> (without .bin)
 
-            expected_preset_name = current_preset.filename.replace(".bin", "")
+            calibration_name = current_info.get("calibration_name")
-            if preset_dir_name != expected_preset_name:
+            preset_filename = current_info.get("preset_filename")
+
+            if not calibration_name or not preset_filename:
+                logger.warning("Invalid current calibration file format")
+                return None
+
+            if preset_filename != current_preset.filename:
                 logger.warning(
                     "Current calibration preset mismatch",
-                    expected=expected_preset_name,
+                    expected=current_preset.filename,
-                    actual=preset_dir_name,
+                    actual=preset_filename,
                 )
-                raise RuntimeError("Current calibration belongs to a different preset")
+                return None
 
             return self.load_calibration_set(current_preset, calibration_name)
         except Exception as exc:  # noqa: BLE001
-            logger.warning("Failed to resolve current calibration", error=repr(exc))
+            logger.warning("Failed to load current calibration", error=repr(exc))
             return None
 
     def clear_current_calibration(self) -> None:
-        """Remove the current calibration symlink."""
+        """Remove the current calibration JSON file."""
-        if self.current_calibration_symlink.exists() or self.current_calibration_symlink.is_symlink():
+        if self.current_calibration_file.exists():
             try:
-                self.current_calibration_symlink.unlink()
+                self.current_calibration_file.unlink()
                 logger.info("Current calibration cleared")
             except Exception as exc:  # noqa: BLE001
                 logger.warning("Failed to clear current calibration", error=repr(exc))

vna_system/core/settings/preset_manager.py

@@ -1,3 +1,4 @@
+import json
 import re
 from dataclasses import dataclass
 from enum import Enum
@@ -52,7 +53,7 @@ class PresetManager:
     <BASE_DIR>/vna_system/binary_input/
         ├─ config_inputs/
         │    └─ *.bin (preset files; configuration encoded in filename)
-        └─ current_input.bin -> config_inputs/<chosen>.bin
+        └─ current_input.json  # Current active preset metadata
 
     Filenames encode parameters, e.g.:
         s11_start100_stop8800_points1000_bw1khz.bin
@@ -69,7 +70,7 @@ class PresetManager:
     def __init__(self, binary_input_dir: Path | None = None) -> None:
         self.binary_input_dir = Path(binary_input_dir or (cfg.BASE_DIR / "vna_system" / "binary_input"))
         self.config_inputs_dir = self.binary_input_dir / "config_inputs"
-        self.current_input_symlink = self.binary_input_dir / "current_input.bin"
+        self.current_input_file = self.binary_input_dir / "current_input.json"
 
         self.config_inputs_dir.mkdir(parents=True, exist_ok=True)
         logger.debug(
@@ -184,43 +185,54 @@ class PresetManager:
 
     def set_current_preset(self, preset: ConfigPreset) -> ConfigPreset:
         """
-        Select a preset by (re)pointing `current_input.bin` to the chosen file.
+        Select a preset by saving it to JSON file.
         """
         src = self.config_inputs_dir / preset.filename
         if not src.exists():
             raise FileNotFoundError(f"Preset file not found: {preset.filename}")
 
-        # Remove any existing link/file
+        # Write current preset info to JSON file
-        if self.current_input_symlink.exists() or self.current_input_symlink.is_symlink():
+        current_info = {
-            try:
+            "filename": preset.filename,
-                self.current_input_symlink.unlink()
+            "mode": preset.mode.value,
-            except Exception as exc:  # noqa: BLE001
+            "start_freq": preset.start_freq,
-                logger.warning("Failed to remove existing current_input.bin", error=repr(exc))
+            "stop_freq": preset.stop_freq,
+            "points": preset.points,
+            "bandwidth": preset.bandwidth
+        }
 
-        # Prefer a relative symlink for portability
+        with self.current_input_file.open("w", encoding="utf-8") as f:
-        try:
+            json.dump(current_info, f, indent=2, ensure_ascii=False)
-            target = src.relative_to(self.binary_input_dir)
-        except ValueError:
-            target = src
 
-        self.current_input_symlink.symlink_to(target)
         logger.info("Current preset set", filename=preset.filename)
         return preset
 
     def get_current_preset(self) -> ConfigPreset | None:
         """
-        Resolve the `current_input.bin` symlink and parse the underlying preset.
+        Load current preset from JSON file.
 
-        Returns None if the symlink is missing or the filename cannot be parsed.
+        Returns None if the file is missing or invalid.
         """
-        if not self.current_input_symlink.exists():
+        if not self.current_input_file.exists():
             return None
 
         try:
-            target = self.current_input_symlink.resolve()
+            with self.current_input_file.open("r", encoding="utf-8") as f:
-            return self._parse_filename(target.name)
+                current_info = json.load(f)
+
+            filename = current_info.get("filename")
+            if not filename:
+                logger.warning("Invalid current preset file format")
+                return None
+
+            # Verify the file still exists
+            if not (self.config_inputs_dir / filename).exists():
+                logger.warning("Current preset file no longer exists", filename=filename)
+                return None
+
+            return self._parse_filename(filename)
         except Exception as exc:  # noqa: BLE001
-            logger.warning("Failed to resolve current preset", error=repr(exc))
+            logger.warning("Failed to load current preset", error=repr(exc))
             return None
 
     def preset_exists(self, preset: ConfigPreset) -> bool:

vna_system/core/settings/reference_manager.py

@@ -63,7 +63,7 @@ class ReferenceManager:
 
     References are stored in the following structure:
     references/
-    ├── current_reference -> symlink to active reference
+    ├── current_reference.json  # Current active reference metadata
     ├── <preset_name>/
     │   ├── <reference_name>/
     │   │   ├── info.json       # Reference metadata
@@ -74,7 +74,7 @@ class ReferenceManager:
 
     def __init__(self):
         self.references_dir = Path(cfg.BASE_DIR) / "references"
-        self.current_reference_symlink = self.references_dir / "current_reference"
+        self.current_reference_file = self.references_dir / "current_reference.json"
 
         # Ensure directory structure exists
         self.references_dir.mkdir(exist_ok=True)
@@ -219,17 +219,16 @@ class ReferenceManager:
             raise ValueError(f"Reference '{name}' not found for preset {preset.filename}")
 
         try:
-            # Remove existing symlink
+            # Write current reference info to JSON file
-            if self.current_reference_symlink.exists() or self.current_reference_symlink.is_symlink():
+            current_info = {
-                self.current_reference_symlink.unlink()
+                "reference_name": name,
+                "preset_filename": preset.filename,
+                "preset_dir": Path(preset.filename).stem,
+                "updated_at": datetime.now().isoformat()
+            }
 
-            # Create relative symlink for portability
+            with self.current_reference_file.open("w", encoding="utf-8") as f:
-            try:
+                json.dump(current_info, f, indent=2, ensure_ascii=False)
-                relative_target = reference_dir.relative_to(self.references_dir)
-            except ValueError:
-                relative_target = reference_dir
-
-            self.current_reference_symlink.symlink_to(relative_target)
 
             logger.info("Set current reference", name=name, preset=preset.filename)
             return True
@@ -249,37 +248,42 @@ class ReferenceManager:
             ReferenceInfo | None: Current reference info, or None if no reference is set
                                     or if the current reference doesn't match the preset
         """
-        if not self.current_reference_symlink.exists():
+        if not self.current_reference_file.exists():
             return None
 
         try:
-            target_dir = self.current_reference_symlink.resolve()
+            with self.current_reference_file.open("r", encoding="utf-8") as f:
+                current_info = json.load(f)
 
-            if not target_dir.exists():
+            reference_name = current_info.get("reference_name")
-                logger.warning("Current reference symlink points to non-existent directory")
+            preset_filename = current_info.get("preset_filename")
+
+            if not reference_name or not preset_filename:
+                logger.warning("Invalid current reference file format")
                 return None
 
-            # Load reference info
+            # Check if reference matches current preset
-            info_file = target_dir / "info.json"
+            if preset_filename != preset.filename:
+                logger.debug(
+                    "Current reference is for different preset",
+                    reference_preset=preset_filename,
+                    current_preset=preset.filename
+                )
+                return None
+
+            # Load full reference info
+            preset_dir = self._get_preset_dir(preset)
+            reference_dir = preset_dir / reference_name
+            info_file = reference_dir / "info.json"
+
             if not info_file.exists():
-                logger.warning("Current reference missing info.json")
+                logger.warning("Current reference missing info.json", name=reference_name)
                 return None
 
             with info_file.open("r", encoding="utf-8") as f:
                 info_data = json.load(f)
 
-            reference_info = ReferenceInfo.from_dict(info_data)
+            return ReferenceInfo.from_dict(info_data)
-
-            # Check if reference matches current preset
-            if reference_info.preset_filename != preset.filename:
-                logger.debug(
-                    "Current reference is for different preset",
-                    reference_preset=reference_info.preset_filename,
-                    current_preset=preset.filename
-                )
-                return None
-
-            return reference_info
 
         except Exception as exc:
             logger.warning("Failed to get current reference", error=repr(exc))
@@ -293,8 +297,8 @@ class ReferenceManager:
             bool: True if cleared successfully
         """
         try:
-            if self.current_reference_symlink.exists() or self.current_reference_symlink.is_symlink():
+            if self.current_reference_file.exists():
-                self.current_reference_symlink.unlink()
+                self.current_reference_file.unlink()
                 logger.info("Cleared current reference")
             return True
         except Exception as exc:

vna_system/references/current_reference

@@ -1 +0,0 @@
-s11_start100_stop8800_points1000_bw1khz/asd