Add functions to determine sample ranges of signals in multi-segment …

…records (#403)

* Add contained_ranges method to calculate sample ranges that contain a signal, in multi-segment records

* Add contained_combined_ranges function

* Add tests for new ranges functions

* Fix logic to account for empty segments and derive some fields in MultiRecord constructor

tests/test_multi_record.py

@@ -0,0 +1,113 @@
+import wfdb
+
+
+class TestMultiRecordRanges:
+    """
+    Test logic that deduces relevant segments/ranges for given signals.
+    """
+
+    def test_contained_ranges_simple_cases(self):
+        record = wfdb.MultiRecord(
+            segments=[
+                wfdb.Record(sig_name=["I", "II"], sig_len=5),
+                wfdb.Record(sig_name=["I", "III"], sig_len=10),
+            ],
+        )
+
+        assert record.contained_ranges("I") == [(0, 15)]
+        assert record.contained_ranges("II") == [(0, 5)]
+        assert record.contained_ranges("III") == [(5, 15)]
+
+    def test_contained_ranges_variable_layout(self):
+        record = wfdb.rdheader(
+            "sample-data/multi-segment/s00001/s00001-2896-10-10-00-31",
+            rd_segments=True,
+        )
+
+        assert record.contained_ranges("II") == [
+            (3261, 10136),
+            (4610865, 10370865),
+            (10528365, 14518365),
+        ]
+        assert record.contained_ranges("V") == [
+            (3261, 918261),
+            (920865, 4438365),
+            (4610865, 10370865),
+            (10528365, 14518365),
+        ]
+        assert record.contained_ranges("MCL1") == [
+            (10136, 918261),
+            (920865, 4438365),
+        ]
+        assert record.contained_ranges("ABP") == [
+            (14428365, 14450865),
+            (14458365, 14495865),
+        ]
+
+    def test_contained_ranges_fixed_layout(self):
+        record = wfdb.rdheader(
+            "sample-data/multi-segment/041s/041s",
+            rd_segments=True,
+        )
+
+        for sig_name in record.sig_name:
+            assert record.contained_ranges(sig_name) == [(0, 2000)]
+
+    def test_contained_combined_ranges_simple_cases(self):
+        record = wfdb.MultiRecord(
+            segments=[
+                wfdb.Record(sig_name=["I", "II", "V"], sig_len=5),
+                wfdb.Record(sig_name=["I", "III", "V"], sig_len=10),
+                wfdb.Record(sig_name=["I", "II", "V"], sig_len=20),
+            ],
+        )
+
+        assert record.contained_combined_ranges(["I", "II"]) == [
+            (0, 5),
+            (15, 35),
+        ]
+        assert record.contained_combined_ranges(["II", "III"]) == []
+        assert record.contained_combined_ranges(["I", "III"]) == [(5, 15)]
+        assert record.contained_combined_ranges(["I", "II", "V"]) == [
+            (0, 5),
+            (15, 35),
+        ]
+
+    def test_contained_combined_ranges_variable_layout(self):
+        record = wfdb.rdheader(
+            "sample-data/multi-segment/s00001/s00001-2896-10-10-00-31",
+            rd_segments=True,
+        )
+
+        assert record.contained_combined_ranges(["II", "V"]) == [
+            (3261, 10136),
+            (4610865, 10370865),
+            (10528365, 14518365),
+        ]
+        assert record.contained_combined_ranges(["II", "MCL1"]) == []
+        assert record.contained_combined_ranges(["II", "ABP"]) == [
+            (14428365, 14450865),
+            (14458365, 14495865),
+        ]
+        assert record.contained_combined_ranges(["II", "V", "ABP"]) == [
+            (14428365, 14450865),
+            (14458365, 14495865),
+        ]
+        assert (
+            record.contained_combined_ranges(["II", "V", "MCL1", "ABP"]) == []
+        )
+
+    def test_contained_combined_ranges_variable_layout(self):
+        record = wfdb.rdheader(
+            "sample-data/multi-segment/041s/041s",
+            rd_segments=True,
+        )
+
+        for sig_1 in record.sig_name:
+            for sig_2 in record.sig_name:
+                if sig_1 == sig_2:
+                    continue
+
+                assert record.contained_combined_ranges([sig_1, sig_2]) == [
+                    (0, 2000)
+                ]

wfdb/io/_header.py

@@ -1,6 +1,6 @@
 import datetime
 import re
-from typing import List, Tuple
+from typing import Collection, List, Tuple
 
 import numpy as np
 import pandas as pd
@@ -858,7 +858,7 @@ def get_sig_name(self):
         """
         if self.segments is None:
             raise Exception(
-                "The MultiRecord's segments must be read in before this method is called. ie. Call rdheader() with rsegment_fieldsments=True"
+                "The MultiRecord's segments must be read in before this method is called. ie. Call rdheader() with rd_segments=True"
             )
 
         if self.layout == "fixed":
@@ -871,6 +871,114 @@ def get_sig_name(self):
 
         return sig_name
 
+    def contained_ranges(self, sig_name: str) -> List[Tuple[int, int]]:
+        """
+        Given a signal name, return the sample ranges that contain signal values,
+        relative to the start of the full record. Does not account for NaNs/missing
+        values.
+
+        This function is mainly useful for variable layout records, but can also be
+        used for fixed-layout records. Only works if the headers from the individual
+        segment records have already been read in.
+
+        Parameters
+        ----------
+        sig_name : str
+            The name of the signal to query.
+
+        Returns
+        -------
+        ranges : List[Tuple[int, int]]
+            Tuple pairs which specify thee sample ranges in which the signal is contained.
+            The second value of each tuple pair will be one beyond the signal index.
+            eg. A length 1000 signal would generate a tuple of: (0, 1000), allowing
+            selection using signal[0:1000].
+
+        """
+        if self.segments is None:
+            raise Exception(
+                "The MultiRecord's segments must be read in before this method is called. ie. Call rdheader() with rd_segments=True"
+            )
+        ranges = []
+        seg_start = 0
+
+        range_start = None
+
+        # TODO: Add shortcut for fixed-layout records
+
+        # Cannot process segments only because missing segments are None
+        # and do not contain length information.
+        for seg_num in range(self.n_seg):
+            seg_len = self.seg_len[seg_num]
+            segment = self.segments[seg_num]
+
+            if seg_len == 0:
+                continue
+
+            # Open signal range
+            if (
+                range_start is None
+                and segment is not None
+                and sig_name in segment.sig_name
+            ):
+                range_start = seg_start
+            # Close signal range
+            elif range_start is not None and (
+                segment is None or sig_name not in segment.sig_name
+            ):
+                ranges.append((range_start, seg_start))
+                range_start = None
+
+            seg_start += seg_len
+
+        # Account for final segment
+        if range_start is not None:
+            ranges.append((range_start, seg_start))
+
+        return ranges
+
+    def contained_combined_ranges(
+        self,
+        sig_names: Collection[str],
+    ) -> List[Tuple[int, int]]:
+        """
+        Given a collection of signal name, return the sample ranges that
+        contain all of the specified signals, relative to the start of the
+        full record. Does not account for NaNs/missing values.
+
+        This function is mainly useful for variable layout records, but can also be
+        used for fixed-layout records. Only works if the headers from the individual
+        segment records have already been read in.
+
+        Parameters
+        ----------
+        sig_names : List[str]
+            The names of the signals to query.
+
+        Returns
+        -------
+        ranges : List[Tuple[int, int]]
+            Tuple pairs which specify thee sample ranges in which the signal is contained.
+            The second value of each tuple pair will be one beyond the signal index.
+            eg. A length 1000 signal would generate a tuple of: (0, 1000), allowing
+            selection using signal[0:1000].
+
+        """
+        # TODO: Add shortcut for fixed-layout records
+
+        if len(sig_names) == 0:
+            return []
+
+        combined_ranges = self.contained_ranges(sig_names[0])
+
+        if len(sig_names) > 1:
+            for name in sig_names[1:]:
+                combined_ranges = util.overlapping_ranges(
+                    combined_ranges, self.contained_ranges(name)
+                )
+
+        return combined_ranges
+
 
 def wfdb_strptime(time_string: str) -> datetime.time:
     """

wfdb/io/record.py

@@ -1080,8 +1080,8 @@ class MultiRecord(BaseRecord, _header.MultiHeaderMixin):
         `datetime.combine(base_date, base_time)`.
     seg_name : str, optional
         The name of the segment.
-    seg_len : int, optional
-        The length of the segment.
+    seg_len : List[int], optional
+        The length of each segment.
     comments : list, optional
         A list of string comments to be written to the header file.
     sig_name : str, optional
@@ -1144,6 +1144,11 @@ def __init__(
         self.seg_len = seg_len
         self.sig_segments = sig_segments
 
+        if segments:
+            self.n_seg = len(segments)
+            if not seg_len:
+                self.seg_len = [segment.sig_len for segment in segments]
+
     def wrsamp(self, write_dir=""):
         """
         Write a multi-segment header, along with headers and dat files
@@ -1184,33 +1189,28 @@ def _check_segment_cohesion(self):
         if self.n_seg != len(self.segments):
             raise ValueError("Length of segments must match the 'n_seg' field")
 
-        for i in range(n_seg):
-            s = self.segments[i]
+        for seg_num, segment in enumerate(self.segments):
 
             # If segment 0 is a layout specification record, check that its file names are all == '~''
-            if i == 0 and self.seg_len[0] == 0:
-                for file_name in s.file_name:
+            if seg_num == 0 and self.seg_len[0] == 0:
+                for file_name in segment.file_name:
                     if file_name != "~":
                         raise ValueError(
                             "Layout specification records must have all file_names named '~'"
                         )
 
             # Sampling frequencies must all match the one in the master header
-            if s.fs != self.fs:
+            if segment.fs != self.fs:
                 raise ValueError(
                     "The 'fs' in each segment must match the overall record's 'fs'"
                 )
 
             # Check the signal length of the segment against the corresponding seg_len field
-            if s.sig_len != self.seg_len[i]:
+            if segment.sig_len != self.seg_len[seg_num]:
                 raise ValueError(
-                    "The signal length of segment "
-                    + str(i)
-                    + " does not match the corresponding segment length"
+                    f"The signal length of segment {seg_num} does not match the corresponding segment length"
                 )
 
-            totalsig_len = totalsig_len + getattr(s, "sig_len")
-
         # No need to check the sum of sig_lens from each segment object against sig_len
         # Already effectively done it when checking sum(seg_len) against sig_len
 

wfdb/io/util.py

@@ -4,7 +4,7 @@
 import math
 import os
 
-from typing import Sequence
+from typing import Sequence, Tuple
 
 
 def lines_to_file(file_name: str, write_dir: str, lines: Sequence[str]):
@@ -99,3 +99,23 @@ def upround(x, base):
 
     """
     return base * math.ceil(float(x) / base)
+
+
+def overlapping_ranges(
+    ranges_1: Tuple[int, int], ranges_2: Tuple[int, int]
+) -> Tuple[int, int]:
+    """
+    Given two collections of integer ranges, return a list of ranges
+    in which both input inputs overlap.
+
+    From: https://stackoverflow.com/q/40367461
+
+    Slightly modified so that if the end of one range exactly equals
+    the start of the other range, no overlap would be returned.
+    """
+    return [
+        (max(first[0], second[0]), min(first[1], second[1]))
+        for first in ranges_1
+        for second in ranges_2
+        if max(first[0], second[0]) < min(first[1], second[1])
+    ]