added agilent rdl

chromatopy/readers/agilent_rdl.py

@@ -0,0 +1,116 @@
+import re
+from typing import Tuple
+
+from chromatopy.model import Chromatogram, Data, Measurement, Peak
+from chromatopy.readers.abstractreader import AbstractReader
+
+
+class AgilentRDLReader(AbstractReader):
+    def read(self):
+        measurements = []
+        for path_id, path in enumerate(self.file_paths):
+            lines = self.read_file(path)
+
+            peak_data, sample_name, signal = self.extract_information(lines)
+
+            peak_data = [
+                self.align_and_concatenate_columns(*pair) for pair in peak_data
+            ]
+            peaks = [self.map_peak(peak) for peak in peak_data]
+
+            sample_name = self.align_and_concatenate_columns(*sample_name)[1]
+
+            wavelength = self.extract_wavelength(signal)
+
+            data = Data(
+                value=self.values[path_id],
+                unit=self.unit,
+                data_type=self.mode,
+            )
+
+            chromatogram = Chromatogram(peaks=peaks, wavelength=wavelength)
+
+            measurements.append(
+                Measurement(
+                    id=f"m{path_id}",
+                    chromatograms=[chromatogram],
+                    temperature=self.temperature,
+                    temperature_unit=self.temperature_unit,
+                    ph=self.ph,
+                    data=data,
+                )
+            )
+
+        if not self.silent:
+            self.print_success(len(measurements))
+
+        return measurements
+
+    @staticmethod
+    def read_file(file_path: str) -> list[str]:
+        with open(file_path, "r") as file:
+            lines = file.readlines()
+
+        return lines
+
+    @staticmethod
+    def extract_information(lines: list[str]) -> Tuple[list[list[str]], list[str], str]:
+        data = []
+        for i, line in enumerate(lines):
+            # Check for first line with float values after space and pipe characters
+            if re.search(r"^\s{2}│\s+\d+\.\d+\s+│", line):
+                line_pair = [line]
+
+                if lines[i + 1].startswith("  │"):
+                    line_pair.append(lines[i + 1])
+                else:
+                    line_pair.append("")
+
+                data.append(line_pair)
+
+            if "│Sample Name     │" in line:
+                sample_name = [line]
+                if lines[i + 1].startswith("   │"):
+                    sample_name.append(lines[i + 1])
+                else:
+                    sample_name.append("")
+                    print("")
+
+            if "│Signal:│" in line:
+                signal = line
+
+        return data, sample_name, signal
+
+    @staticmethod
+    def extract_wavelength(line: str) -> int | None:
+        pattern = r"Sig=(\d+)"
+
+        match = re.search(pattern, line)
+        if match:
+            return int(match.group(1))
+        else:
+            return None
+
+    @staticmethod
+    def align_and_concatenate_columns(row1, row2):
+        # Split each string by the vertical bar '│' and strip whitespace from each column
+        row1_columns = [col.strip() for col in re.split(r"│", row1) if col]
+        row2_columns = [col.strip() for col in re.split(r"│", row2) if col]
+
+        # Concatenate aligned columns
+        aligned_columns = [
+            f"{col1}{col2}".strip() for col1, col2 in zip(row1_columns, row2_columns)
+        ]
+
+        return aligned_columns[1:-1]
+
+    @staticmethod
+    def map_peak(peak_list: list[str]) -> Peak:
+        return Peak(
+            retention_time=float(peak_list[0]),
+            type=peak_list[1],
+            width=float(peak_list[2]),
+            area=float(peak_list[3]),
+            amplitude=float(peak_list[4]),
+            percent_area=float(peak_list[5]),
+        )

docs/examples/data/agilent_rdl/M2_MJ_100_min.txt

@@ -0,0 +1,40 @@
+┌──────────────────────────────────────────────────────────────────────────────┐
+│Cross Sequence Summary Report                                                 │
+└──────────────────────────────────────────────────────────────────────────────┘
+   ┌────────────────┬──────────────────────────────────────────────────────────┐
+   │Sample Name     │M2_MJ_                                                    │
+   │                │100_min                                                   │
+   └────────────────┴──────────────────────────────────────────────────────────┘
+  ┌───────┬────────────────────────────────────────────────────────────────────┐
+  │Signal:│DAD1A,Sig=254,4  Ref=360,100                                        │
+  └───────┴────────────────────────────────────────────────────────────────────┘
+  ┌───────┬───┬────────┬────────┬───────┬────────┬─────────────────────────────┐
+  │    RT │Typ│  Width │   Area │ Height│  Area% │Name                         │
+  │ [min] │e  │  [min] │        │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 0.698 │BV │ 0.4062 │    53. │ 7.2642│ 0.3671 │                             │
+  │       │   │        │   0992 │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 1.169 │VV │ 0.8468 │  6094. │   783.│    42. │AMP@1,169min                 │
+  │       │   │        │   3336 │   0775│   1289 │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 2.756 │VB │ 0.4315 │    14. │ 1.9341│ 0.0982 │                             │
+  │       │   │        │   2114 │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 3.331 │BV │ 0.7823 │  7620. │   925.│    52. │ADP@3,327min                 │
+  │       │   │        │   7030 │   5433│   6804 │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 3.974 │VB │ 1.5648 │   381. │    55.│ 2.6397 │                             │
+  │       │   │        │   8593 │   0016│        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 5.770 │BB │ 1.0452 │   301. │    22.│ 2.0856 │ATP@5,720min                 │
+  │       │   │        │   7014 │   1066│        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │       │   │    Sum │ 14465. │       │        │                             │
+  │       │   │        │   9079 │       │        │                             │
+  └───────┴───┴────────┴────────┴───────┴────────┴─────────────────────────────┘
+┌───────────────────────────┬────────────────────────────────┬─────────────────┐
+│D:\CDSProjects\JNS\Report  │     Printed:  2024-10-20       │    Page 1 of 1  │
+│Templates\Export_for_      │        16:25:44+02:00          │                 │
+│python.rdl [Rev. 2.0]      │                                │                 │
+════════════════════════════════════════════════════════════════════════════════