From a1a7b411f1f054152cfb3e50623227ef10c718dc Mon Sep 17 00:00:00 2001
From: "J.A. de Jong - Redu-Sone B.V., ASCEE V.O.F" <j.a.dejong@ascee.nl>
Date: Tue, 16 May 2023 12:12:36 +0200
Subject: [PATCH] Updates and bugfixes on fromnpy in Measurement

---
 src/lasp/lasp_measurement.py | 62 ++++++++++++++++++++++++++----------
 1 file changed, 46 insertions(+), 16 deletions(-)

diff --git a/src/lasp/lasp_measurement.py b/src/lasp/lasp_measurement.py
index cbe0d91..9f05a3b 100644
--- a/src/lasp/lasp_measurement.py
+++ b/src/lasp/lasp_measurement.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+from __future__ import annotations
 """!
 Author: J.A. de Jong - ASCEE
 
@@ -113,7 +114,7 @@ class IterRawData:
         nblocks = fa.shape[0]
         blocksize = fa.shape[1]
         self.blocksize = blocksize
-        nchannels = fa.shape[2]
+        # nchannels = fa.shape[2]
         self.channels = channels
 
         self.istart = kwargs.pop('istart', 0)
@@ -143,7 +144,7 @@ class IterRawData:
         """Return the next block."""
         fa = self.fa
 
-        nblocks_to_return = self.lastblock-self.firstblock+1
+        # nblocks_to_return = self.lastblock-self.firstblock+1
 
         block = self.firstblock + self.i
 
@@ -162,7 +163,7 @@ class IterRawData:
         # print(f'block: {block}, starto: {start_offset}, stopo {stop_offset}')
 
         self.i += 1
-        return self.fa[block, start_offset:stop_offset, :][:, self.channels]
+        return fa[block, start_offset:stop_offset, :][:, self.channels]
 
 
 class IterData(IterRawData):
@@ -771,23 +772,32 @@ class Measurement:
                 samplerate,
                 sensitivity,
                 mfn,
-                timestamp=None):
-        """Converts a numpy array to a LASP Measurement file, opens the
-        associated Measurement object and returns it. The measurement file will
-        have the same file name as the txt file, except with h5 extension.
+                timestamp=None,
+                qtys: List[SIQtys] = None,
+                channelNames: List[str] = None,
+                force=False) -> Measurement:
+        """
+        Creates a LASP measurement file from input numpy array data.
+        Opens the associated Measurement object and returns it.
 
         Args:
             data: Numpy array, first column is sample, second is channel. Can
-            also be specified with a single column for single-channel data
+            also be specified with a single column for single-channel data.
+            
             samplerate: Sampling frequency in [Hz]
-            sensitivity: 1D array of channel sensitivities [Pa^-1]
-            mfn: Filepath where measurement file is stored.
+            
+            sensitivity: 1D array of channel sensitivities in [U^-1], where U is
+            the recorded unit.
+            
+            mfn: Filepath of the file where the data is stored.
+            
             timestamp: If given, a custom timestamp for the measurement
-            (integer containing seconds since epoch). If not given, the
-            timestamp is obtained from the last modification time.
-            delimiter: Column delimiter
-            firstcoltime: If true, the first column is the treated as the
-            sample time.
+            (integer containing seconds since epoch).
+
+            qtys: If a list of physical quantity data is given here
+
+            channelNames: Name of the channels
+            
             force: If True, overwrites existing files with specified `mfn`
             name.
         """
@@ -801,24 +811,44 @@ class Measurement:
         if data.ndim != 2:
             data = data[:, np.newaxis]
 
+
         try:
             len(sensitivity)
         except:
             raise ValueError('Sensitivity should be given as array-like data type')
         sensitivity = np.asarray(sensitivity)
 
-
         nchannels = data.shape[1]
         if nchannels != sensitivity.shape[0]:
             raise ValueError(
                 f'Invalid sensitivity length given. Should be: {nchannels}')
 
+        if channelNames is not None:
+            if len(channelNames) != nchannels:
+                raise RuntimeError("Illegal length of channelNames list given")
+
+        if qtys is None:
+            qtys = [SIQtys.AP]*nchannels
+        else:
+            if len(qtys) != nchannels:
+                raise RuntimeError("Illegal length of qtys list given")
+
+        qtyvals = [qty.value for qty in qtys]
+
         with h5.File(mfn, 'w') as hf:
             hf.attrs['samplerate'] = samplerate
             hf.attrs['sensitivity'] = sensitivity
             hf.attrs['time'] = timestamp
             hf.attrs['blocksize'] = 1
             hf.attrs['nchannels'] = nchannels
+
+            # Add physical quantity indices
+            hf.attrs['qtys_enum_idx'] = [qtyval.toInt() for qtyval in qtyvals]
+
+            # Add channel names in case given
+            if channelNames is not None:
+                hf.attrs['channelNames'] = channelNames
+
             ad = hf.create_dataset('audio', (1, data.shape[0], data.shape[1]),
                                    dtype=data.dtype,
                                    maxshape=(1, data.shape[0], data.shape[1]),