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[METEOR-1230][fix] store power correctly for each channel in metadata #2947

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[METEOR-1230][fix] store power correctly for each channel in metadata #2947

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25 changes: 22 additions & 3 deletions src/odemis/dataio/test/tiff_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2156,6 +2156,7 @@ def testFindImageGroupsAcquiredMultiChannelZStack(self):
model.MD_EXP_TIME: 1.2, # s
model.MD_IN_WL: (500e-9, 522e-9), # m
model.MD_OUT_WL: (400e-9, 450e-9), # m
model.MD_LIGHT_POWER: 0.140, # W
},
{model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake hw",
Expand All @@ -2165,9 +2166,10 @@ def testFindImageGroupsAcquiredMultiChannelZStack(self):
model.MD_BINNING: (1, 1), # px, px
model.MD_PIXEL_SIZE: (1e-6, 1e-6), # m/px
model.MD_POS: (13.7e-3, -30e-3), # m
model.MD_EXP_TIME: 1, # s
model.MD_EXP_TIME: 2, # s
model.MD_IN_WL: (590e-9, 620e-9), # m
model.MD_OUT_WL: (520e-9, 550e-9), # m
model.MD_LIGHT_POWER: 0.240, # W
},
{model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake hw",
Expand All @@ -2177,9 +2179,10 @@ def testFindImageGroupsAcquiredMultiChannelZStack(self):
model.MD_BINNING: (1, 1), # px, px
model.MD_PIXEL_SIZE: (1e-6, 1e-6), # m/px
model.MD_POS: (13.7e-3, -30e-3), # m
model.MD_EXP_TIME: 1, # s
model.MD_EXP_TIME: 1.5, # s
model.MD_IN_WL: (600e-9, 630e-9), # m
model.MD_OUT_WL: (620e-9, 650e-9), # m
model.MD_LIGHT_POWER: 0.350, # W
},
]
# create 3 greyscale images with Z stacks of same size
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You can further improve this test by having 2 Z stacks, with something like:

        for md in metadata.copy():
            md2 = md.copy()
            md2[model.MD_POS] = (1.7e-3, -97e-3)
            md2[model.MD_LIGHT_POWER] += 1
            metadata.append(md2)

It fails due to the LightSource ID being incorrect, as you can see in the TIFF metadata:

        <LightEmittingDiode ID="LightSource:0" Power="140.000000000000000" PowerUnit="mW" />
        <LightEmittingDiode ID="LightSource:1" Power="240.000000000000000" PowerUnit="mW" />
        <LightEmittingDiode ID="LightSource:2" Power="350.000000000000000" PowerUnit="mW" />
        <LightEmittingDiode ID="LightSource:0" Power="1140.000000000000227" PowerUnit="mW" />
        <LightEmittingDiode ID="LightSource:1" Power="1240.000000000000000" PowerUnit="mW" />
        <LightEmittingDiode ID="LightSource:2" Power="1350.000000000000000" PowerUnit="mW" />
        <Detector ID="Detector:0" Model="fake hw" />
        <Detector ID="Detector:9" Model="fake hw" />

Expand Down Expand Up @@ -2219,7 +2222,7 @@ def testFindImageGroupsAcquiredMultiChannelZStack(self):
for k in range(nb_t):
combinations_zc.append((i, j, k))

tiff_data_elements = root.findall('.//{http://www.openmicroscopy.org/Schemas/OME/2012-06}TiffData')
tiff_data_elements = root.findall('.//{http://www.openmicroscopy.org/Schemas/OME/2016-06}TiffData')
for ind, element in enumerate(tiff_data_elements):
tiffdata = element.attrib
if int(tiffdata["IFD"]) < ifd_max:
Expand All @@ -2243,6 +2246,22 @@ def testFindImageGroupsAcquiredMultiChannelZStack(self):
res = (1,) * (5 - len(shape)) + shape
self.assertEqual(im.shape, res)

# validate the metadata after re-opening the file
exclude_keys = [model.MD_SW_VERSION, model.MD_ACQ_DATE] # md that is not saved in the file
# note: acq_date causes timezone issues when comparing, so skipped in this test
for i, md in enumerate(metadata):
for key, value in md.items():
if key in exclude_keys:
continue
self.assertIn(key, rdata[i].metadata)

if isinstance(value, (tuple, list)):
numpy.testing.assert_array_almost_equal(value, rdata[i].metadata[key])
elif isinstance(value, float):
self.assertAlmostEqual(value, rdata[i].metadata[key], delta=1e-5)
else:
self.assertEqual(value, rdata[i].metadata[key])

def testAcquisitionDataTIFFLargerFile(self):

def getSubData(dast, zoom, rect):
Expand Down
25 changes: 23 additions & 2 deletions src/odemis/dataio/tiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -495,7 +495,23 @@ def _convertToOMEMD(images, multiple_files=False, findex=None, fname=None, uuids
description.text = da0.metadata[model.MD_HW_NOTE]

# light source must come before detector for valid ome-xml
if (model.MD_LIGHT_POWER in da0.metadata or
# meteor multi-channel lightsource
if model.MD_LIGHT_POWER in da0.metadata and (
model.MD_IN_WL in da0.metadata or model.MD_OUT_WL in da0.metadata
):
# TODO: what is the best way to check if image is meteor?
# add a light source for each channel, as they can have different power
for gdid, gr in enumerate(g):

obj = ET.Element("LightEmittingDiode",
attrib={"ID": "LightSource:%d" % gdid})
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Using just the gdid here is incorrect, as there can be several groups of zstacks. So, something like did + gdid would more likely work in every case.

if model.MD_LIGHT_POWER in gr.metadata:
pwr = gr.metadata[model.MD_LIGHT_POWER] * 1e3 # in mW
obj.attrib["Power"] = "%.15f" % pwr
obj.attrib["PowerUnit"] = "mW"
light_sources.append(obj)

elif (model.MD_LIGHT_POWER in da0.metadata or
model.MD_EBEAM_CURRENT in da0.metadata or
model.MD_EBEAM_CURRENT_TIME in da0.metadata
):
Expand Down Expand Up @@ -1611,7 +1627,12 @@ def _addImageElement(root, das, ifd, rois, fname=None, fuuid=None):

# TODO: non-standard metadata, treat it differently for different detectors
cot = da.metadata.get(model.MD_EBEAM_CURRENT_TIME)
if attrib or cot or model.MD_LIGHT_POWER in da.metadata:

# support light source per channel (meteor)
if not (attrib and cot) and model.MD_LIGHT_POWER in da.metadata:
attrib["ID"] = "LightSource:%d" % subid
ds = ET.SubElement(chan, "LightSourceSettings", attrib=attrib)
elif attrib or cot or model.MD_LIGHT_POWER in da.metadata:
attrib["ID"] = "LightSource:%d" % ifd
ds = ET.SubElement(chan, "LightSourceSettings", attrib=attrib)
# This is a non-standard metadata, it defines the emitter, which
Expand Down
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