1862 import APH file in read_cropreporter

docs/photosynthesis_read_cropreporter.md

@@ -22,7 +22,7 @@ PSII_data instance containing [xarray DataArrays](http://xarray.pydata.org/en/st
     - Measurements from chlorophyll fluorescence are stored in the attribute `chlorophyll` and include a chlorophyll fluorescence frame (Chl) stored as NumPy array/ndarray. The Fdark frame, if collected, is not stored.
     - Green fluorescence protein (GFP) measurements are stored in the attribute `gfp` and include frames for dark fluorescence (Fdark), GFP fluorescence (GFP, 525 nm), and autofluorescence (Auto, 585 nm).
     - Red fluorescence protein (RFP) measurements are stored in the attribute `rfp` and include frames for dark fluorescence (Fdark) and RFP fluorescence (585 nm).
-    - Alpha light absorption coefficient (APH) measurements are stored in the attribute `aph` and include reflected light frames for red (640 nm) and far-red (732 nm) wavelengths.
+    - Alpha light absorption coefficient (APH) measurements are stored in the attribute `aph` and include reflected light frames for red (640 nm) and far-red (732 nm) wavelengths. `ps.aph` is a NumPy array/ndarray with shape (height, width, 2), where index 0 is the red frame and index 1 is the far-red frame. The Fdark frame, if collected, is not stored. 
     - Spectral measurements are stored as a PlantCV [Spectral_data](Spectral_data.md) object in the attribute
       `spectral`. Frames are stored by reflectance wavelength and can include: blue (475nm), green (550nm), red (640nm),
       green2 (540nm), far-red (710nm), and near-infrared (770nm).
@@ -81,6 +81,6 @@ ps.ojip_dark.plot(col='frame_label', col_wrap=4)
 
 **Alpha light absorption coefficient (APH) measurements**
 
-![Screenshot](img/documentation_images/photosynthesis_read_cropreporter/6_aph_frames.png)
+![Screenshot](img/documentation_images/photosynthesis_read_cropreporter/6_APH-frames.png)
 
 **Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/main/plantcv/plantcv/photosynthesis/read_cropreporter.py)

plantcv/plantcv/photosynthesis/read_cropreporter.py

@@ -579,42 +579,47 @@ def _process_rfp_data(ps, metadata):
 
 
 def _process_aph_data(ps, metadata):
-    """
-    Create an xarray DataArray for an APH dataset.
+    """Read APH dataset and keep the Red and FarRed frames as a NumPy array.
 
     Parameters
     ----------
     ps : plantcv.plantcv.classes.PSII_data
         PSII_data instance.
     metadata : dict
         INF file metadata dictionary.
-
     """
     bin_filepath = _dat_filepath(dataset="APH", datapath=ps.datapath, filename=ps.filename)
+
     if os.path.exists(bin_filepath):
-        img_cube, frame_labels, frame_nums = _read_dat_file(dataset="APH", filename=bin_filepath,
-                                                            height=int(metadata["ImageRows"]),
-                                                            width=int(metadata["ImageCols"]))
-        frame_labels = ["Red", "FarRed"]
-        aph = xr.DataArray(
-            data=img_cube,
-            dims=('x', 'y', 'frame_label'),
-            coords={'frame_label': frame_labels,
-                    'frame_num': ('frame_label', frame_nums)},
-            name='aph'
-        )
-        aph.attrs["long_name"] = "Alpha Light absorption coefficient (Reflection) (640nm Red, 732nm FarRed)"
-        aph.attrs["dark_comp_on"] = int(metadata.get("AphDarkCompOn", metadata.get("AlphaDarkCompOn", "0")))
-        aph.attrs["gain_red"] = float(metadata.get("AphGainRed", metadata.get("AlphaGainRed", "nan")))
-        aph.attrs["gain_farred"] = float(metadata.get("AphGainFarRed", metadata.get("AlphaGainFarRed", "nan")))
-        ps.add_data(aph)
+        # Read the raw data cube (contains Fdark, Red, and FarRed or just Red and FarRed)
+        img_cube, _, _ = _read_dat_file(dataset="APH", filename=bin_filepath,
+                                        height=int(metadata["ImageRows"]),
+                                        width=int(metadata["ImageCols"]))
 
-        _debug(
-            visual=ps.aph,
-            filename=os.path.join(params.debug_outdir, f"{str(params.device)}_APH-frames.png"),
-            col='frame_label',
-            col_wrap=int(np.ceil(ps.aph.frame_label.size / 4))
+        # The APH file typically has: index 0 = Fdark, index 1 = Red, index 2 = FarRed.
+        # Some acquisitions may only contain two frames (e.g. no dark frame).
+        # Select the Red and FarRed frames based on the number of frames present.
+        # Use the last 2 frames as Red and FarRed:
+        # - When there are 3 frames, indices are [0]=Fdark, [1]=Red, [2]=FarRed -> use indices 1 and 2.
+        # - When there are 2 frames, indices are [0]=Red, [1]=FarRed -> use indices 0 and 1.
+        num_frames = img_cube.shape[2]
+        if num_frames < 2:
+            raise RuntimeError(f"APH DAT file contains {num_frames} frame(s); expected at least 2 (Red and FarRed).")
+        aph_frames = img_cube[:, :, num_frames - 2:num_frames]
+
+        # Store as a standard attribute
+        ps.aph = aph_frames
+
+        # Debugging — wrap in a temporary DataArray so frame labels appear in the plot
+        aph_debug = xr.DataArray(
+            data=ps.aph,
+            dims=('x', 'y', 'frame_label'),
+            coords={'frame_label': ['Red', 'FarRed']}
         )
+        _debug(visual=aph_debug,
+               filename=os.path.join(params.debug_outdir, f"{str(params.device)}_APH-frames.png"),
+               col='frame_label',
+               col_wrap=2)
 
 
 def _dat_filepath(dataset, datapath, filename):

tests/plantcv/photosynthesis/test_read_cropreporter.py

@@ -139,6 +139,28 @@ def test_read_cropreporter_aph_only(photosynthesis_test_data, tmpdir):
     assert ps.aph.shape[2] == 2  # Red + FarRed
 
 
+def test_read_cropreporter_aph_insufficient_frames(photosynthesis_test_data, tmpdir, monkeypatch):
+    """Test that APH import raises RuntimeError when DAT file contains fewer than 2 frames."""
+    cache_dir = tmpdir.mkdir("sub_aph_err")
+    inf_dest = os.path.join(cache_dir, "HDR_2025-12-12_tob1_20251212205712029.INF")
+    dat_dest = os.path.join(cache_dir, "APH_2025-12-12_tob1_20251212205712029.DAT")
+    shutil.copyfile(photosynthesis_test_data.cropreporter_aph, inf_dest)
+    aph_dat = photosynthesis_test_data.cropreporter_aph.replace("HDR", "APH").replace("INF", "DAT")
+    shutil.copyfile(aph_dat, dat_dest)
+    # Override image dimensions so monkeypatched data is the right size
+    with open(inf_dest, "a") as f:
+        f.write("\nImageRows=10")
+        f.write("\nImageCols=10")
+    # Return only 1 frame worth of data (10 * 10 * 1 = 100) to trigger the error
+    monkeypatch.setattr(np, "fromfile", lambda *args, **kwargs: np.ones(100, dtype=np.uint16))
+    error_raised = False
+    try:
+        read_cropreporter(filename=inf_dest)
+    except RuntimeError:
+        error_raised = True
+    assert error_raised
+
+
 def test_read_cropreporter_pmt_only_9_labels(photosynthesis_test_data, tmpdir):
     """Test PMT (PAM Time) import with 9 frames."""
     # Create a test tmp directory