deploy: phasorpy/phasorpy@6c6a62a

Author: cgohlke

docs/main/_downloads/18de1ed1105dda1f0c5220a278448c20/phasorpy_phasor_from_lifetime.zip

@@ -108,7 +108,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Apparent single lifetimes are calculated from the calibrated phasor\ncoordinates and compared to the \"Fast FLIM\" lifetimes (average photon\narrival times) calculated by LAS X software:\n\n"
+        "Apparent single lifetimes are calculated from the calibrated phasor\ncoordinates and compared to the \"Fast FLIM\" lifetimes (average photon\narrival times) calculated by LAS X software. The Fast FLIM lifetimes are\ncorrected for the IRF position, which is extracted from metadata:\n\n"
       ]
     },
     {
@@ -119,14 +119,14 @@
       },
       "outputs": [],
       "source": [
-        "phase_lifetime, modulation_lifetime = phasor_to_apparent_lifetime(\n    real, imag, frequency\n)\n\nfastflim_lifetime = lifetime_from_lif(fetch(filename))[0]\nfastflim_lifetime[numpy.isnan(mean)] = numpy.nan\n\nplot_histograms(\n    phase_lifetime,\n    modulation_lifetime,\n    fastflim_lifetime,\n    range=(0, 10),\n    bins=100,\n    alpha=0.66,\n    xlabel='Lifetime (ns)',\n    ylabel='Count',\n    labels=[\n        'Phase lifetime',\n        'Modulation lifetime',\n        'Fast FLIM lifetime from LIF',\n    ],\n    title='Lifetime histograms',\n)"
+        "phase_lifetime, modulation_lifetime = phasor_to_apparent_lifetime(\n    real, imag, frequency\n)\n\nfastflim_lifetime, _, _, attrs = lifetime_from_lif(fetch(filename))\nfastflim_lifetime[numpy.isnan(mean)] = numpy.nan\n\nfrequency = attrs['frequency']\nreference = attrs['flim_phasor_channels'][0]['AutomaticReferencePhase']\nfastflim_lifetime -= math.radians(reference) / (2 * math.pi) / frequency * 1000\n\nplot_histograms(\n    phase_lifetime,\n    modulation_lifetime,\n    fastflim_lifetime,\n    range=(0, 10),\n    bins=100,\n    alpha=0.6,\n    xlabel='Lifetime (ns)',\n    ylabel='Count',\n    labels=[\n        'Phase lifetime',\n        'Modulation lifetime',\n        'Fast FLIM lifetime',\n    ],\n    title='Lifetime histograms',\n)"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "The apparent single lifetimes from phase and modulation do not exactly match.\nMost likely there is more than one lifetime component in the sample.\n\n"
+        "The apparent single lifetimes from phase and modulation do not exactly match\nand the Fast FLIM lifetimes are in between them.\nMost likely there is more than one lifetime component in the sample.\n\n"
       ]
     },
     {
@@ -241,7 +241,7 @@
       },
       "outputs": [],
       "source": [
-        "plot_histograms(\n    phasor_to_apparent_lifetime(real, imag, frequency)[0],\n    phase_lifetime,\n    range=(0, 10),\n    bins=100,\n    alpha=0.66,\n    xlabel='Lifetime (ns)',\n    ylabel='Count',\n    labels=['Phase lifetime from PTU', 'Phase lifetime from LIF'],\n    title='Lifetime histograms',\n)"
+        "plot_histograms(\n    phasor_to_apparent_lifetime(real, imag, frequency)[0],\n    phase_lifetime,\n    range=(0, 10),\n    bins=100,\n    alpha=0.6,\n    xlabel='Lifetime (ns)',\n    ylabel='Count',\n    labels=['Phase lifetime from PTU', 'Phase lifetime from LIF'],\n    title='Lifetime histograms',\n)"
       ]
     },
     {
@@ -701,7 +701,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "sphinx_gallery_thumbnail_number = 3\nmypy: allow-untyped-defs, allow-untyped-calls\nmypy: disable-error-code=\"arg-type\"\n\n"
+        "sphinx_gallery_thumbnail_number = 11\nmypy: allow-untyped-defs, allow-untyped-calls\nmypy: disable-error-code=\"arg-type\"\n\n"
       ]
     }
   ],

docs/main/_downloads/1b3c132ff7b40bb13bb60712fdfbc4bc/phasorpy_io.ipynb

@@ -114,34 +114,40 @@
 # %%
 # Apparent single lifetimes are calculated from the calibrated phasor
 # coordinates and compared to the "Fast FLIM" lifetimes (average photon
-# arrival times) calculated by LAS X software:
+# arrival times) calculated by LAS X software. The Fast FLIM lifetimes are
+# corrected for the IRF position, which is extracted from metadata:
 
 phase_lifetime, modulation_lifetime = phasor_to_apparent_lifetime(
     real, imag, frequency
 )
 
-fastflim_lifetime = lifetime_from_lif(fetch(filename))[0]
+fastflim_lifetime, _, _, attrs = lifetime_from_lif(fetch(filename))
 fastflim_lifetime[numpy.isnan(mean)] = numpy.nan
 
+frequency = attrs['frequency']
+reference = attrs['flim_phasor_channels'][0]['AutomaticReferencePhase']
+fastflim_lifetime -= math.radians(reference) / (2 * math.pi) / frequency * 1000
+
 plot_histograms(
     phase_lifetime,
     modulation_lifetime,
     fastflim_lifetime,
     range=(0, 10),
     bins=100,
-    alpha=0.66,
+    alpha=0.6,
     xlabel='Lifetime (ns)',
     ylabel='Count',
     labels=[
         'Phase lifetime',
         'Modulation lifetime',
-        'Fast FLIM lifetime from LIF',
+        'Fast FLIM lifetime',
     ],
     title='Lifetime histograms',
 )
 
 # %%
-# The apparent single lifetimes from phase and modulation do not exactly match.
+# The apparent single lifetimes from phase and modulation do not exactly match
+# and the Fast FLIM lifetimes are in between them.
 # Most likely there is more than one lifetime component in the sample.
 
 # %%
@@ -251,7 +257,7 @@
     phase_lifetime,
     range=(0, 10),
     bins=100,
-    alpha=0.66,
+    alpha=0.6,
     xlabel='Lifetime (ns)',
     ylabel='Count',
     labels=['Phase lifetime from PTU', 'Phase lifetime from LIF'],
@@ -742,6 +748,6 @@
 plot_phasor(real, imag, frequency=80.0, allquadrants=True, title=filename)
 
 # %%
-# sphinx_gallery_thumbnail_number = 3
+# sphinx_gallery_thumbnail_number = 11
 # mypy: allow-untyped-defs, allow-untyped-calls
 # mypy: disable-error-code="arg-type"