From 900b60cdfb6aec114a23515da2df21a86d81dff0 Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Tue, 17 Feb 2026 11:31:39 +0100 Subject: [PATCH 1/7] Remove NXxas_mode --- applications/NXxas_new.nxdl.xml | 3 --- 1 file changed, 3 deletions(-) diff --git a/applications/NXxas_new.nxdl.xml b/applications/NXxas_new.nxdl.xml index 1c2df512ee..1c53cf04b6 100644 --- a/applications/NXxas_new.nxdl.xml +++ b/applications/NXxas_new.nxdl.xml @@ -45,9 +45,6 @@ - - - Excited element From ef88cf6854b16d812c6757b5f1ab0abe5c73859b Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Tue, 17 Feb 2026 12:20:50 +0100 Subject: [PATCH 2/7] Add transmission subclass --- applications/NXxas_new.nxdl.xml | 16 ++++-- applications/NXxas_transmission.nxdl.xml | 71 ++++++++++++++++++++++++ 2 files changed, 82 insertions(+), 5 deletions(-) create mode 100644 applications/NXxas_transmission.nxdl.xml diff --git a/applications/NXxas_new.nxdl.xml b/applications/NXxas_new.nxdl.xml index 1c53cf04b6..f9957a463e 100644 --- a/applications/NXxas_new.nxdl.xml +++ b/applications/NXxas_new.nxdl.xml @@ -3,7 +3,7 @@ + + + The intensity of the spectrum is the absorption coefficient :math:`\mu(E)` + given by: + + .. math:: \mu(E)t = -\ln(I/I_0) + + where :math:`I` is the intensity of the transmitted beam, :math:`I_0` + is the intensity of the incident beam, and :math:`t` is the thickness + of the sample. + + The intensity of the reference sample is given by :math:`I_{ref}`. + + + + Official NeXus NXDL schema to which this file conforms. + + + + + + + The intensity of the incident beam, before the sample. + + + + + + + + The intensity of the transmitted beam, after the sample. + + + + + + + + The intensity of the reference sample. + + + + + + + From 24678b64a65724dae14a001a1748389119318b87 Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Tue, 17 Feb 2026 14:07:12 +0100 Subject: [PATCH 3/7] Add the intensity field for transmission --- applications/NXxas_transmission.nxdl.xml | 25 +++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/applications/NXxas_transmission.nxdl.xml b/applications/NXxas_transmission.nxdl.xml index 0c7c443650..e4a4d26153 100644 --- a/applications/NXxas_transmission.nxdl.xml +++ b/applications/NXxas_transmission.nxdl.xml @@ -25,16 +25,19 @@ xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd "> - The intensity of the spectrum is the absorption coefficient :math:`\mu(E)` - given by: + In transmission, the absorption coefficient :math:`\mu(E)` given by the + Beer-Lambert law: .. math:: \mu(E)t = -\ln(I/I_0) - where :math:`I` is the intensity of the transmitted beam, :math:`I_0` - is the intensity of the incident beam, and :math:`t` is the thickness - of the sample. - - The intensity of the reference sample is given by :math:`I_{ref}`. + where :math:`I` is the intensity of the transmitted beam, :math:`I_0` is + the intensity of the incident beam, and :math:`t` is the thickness of the + sample. + + In many experimental setups, a third detector is placed downstream of the + main sample and a secondary reference material (typically a high-purity + metal foil) to record :math:`I_{ref}`, the reference intensity, which is + used to correct for beam fluctuations. @@ -43,6 +46,14 @@ + + + The absorption coefficient :math:`\mu(E)` defined above. + + + + + The intensity of the incident beam, before the sample. From 33a4a7b51b678b85682bb3a405435a110b9551c8 Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Tue, 17 Feb 2026 14:27:24 +0100 Subject: [PATCH 4/7] Formatting --- applications/NXxas_transmission.nxdl.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/applications/NXxas_transmission.nxdl.xml b/applications/NXxas_transmission.nxdl.xml index e4a4d26153..aef76a5d7e 100644 --- a/applications/NXxas_transmission.nxdl.xml +++ b/applications/NXxas_transmission.nxdl.xml @@ -25,7 +25,7 @@ xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd "> - In transmission, the absorption coefficient :math:`\mu(E)` given by the + In transmission, the absorption coefficient :math:`\mu(E)` is given by the Beer-Lambert law: .. math:: \mu(E)t = -\ln(I/I_0) @@ -34,10 +34,10 @@ the intensity of the incident beam, and :math:`t` is the thickness of the sample. - In many experimental setups, a third detector is placed downstream of the - main sample and a secondary reference material (typically a high-purity - metal foil) to record :math:`I_{ref}`, the reference intensity, which is - used to correct for beam fluctuations. + In many experimental setups, a third detector is can be placed downstream + of the main sample and a secondary reference material (typically a + high-purity metal foil) to record :math:`I_{ref}`, the reference + intensity, which is used to correct for beam fluctuations. From 6dd40899ab23f5d28f8f576f1dcbbc4306545e77 Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Sun, 22 Feb 2026 19:57:04 +0100 Subject: [PATCH 5/7] Update transmission and add TFY --- applications/NXxas_tfy.nxdl.xml | 69 +++++++++++++++++++ ...smission.nxdl.xml => NXxas_trans.nxdl.xml} | 30 +++++++- 2 files changed, 98 insertions(+), 1 deletion(-) create mode 100644 applications/NXxas_tfy.nxdl.xml rename applications/{NXxas_transmission.nxdl.xml => NXxas_trans.nxdl.xml} (70%) diff --git a/applications/NXxas_tfy.nxdl.xml b/applications/NXxas_tfy.nxdl.xml new file mode 100644 index 0000000000..23ba452c94 --- /dev/null +++ b/applications/NXxas_tfy.nxdl.xml @@ -0,0 +1,69 @@ + + + + + + In total fluorescence yield (TFY), the absorption coefficient :math:`\mu(E)` is + proportional to the ratio of the intensity of the emitted fluorescence + :math:`I_f` and the incident beam :math:`I_0`: + + .. math:: \mu(E) \propto I_f/I_0 + + where :math:`I_f` is the intensity of the fluorescence emission, and :math:`I_0` is + the intensity of the incident beam. + + + + Official NeXus NXDL schema to which this file conforms. + + + + + + + The absorption coefficient :math:`\mu(E)` defined above. + + + + + + + + The intensity of the incident beam. + + + + + + + + The intensity of the total fluorescence emission. + + + + + + + diff --git a/applications/NXxas_transmission.nxdl.xml b/applications/NXxas_trans.nxdl.xml similarity index 70% rename from applications/NXxas_transmission.nxdl.xml rename to applications/NXxas_trans.nxdl.xml index aef76a5d7e..3b64c91b6f 100644 --- a/applications/NXxas_transmission.nxdl.xml +++ b/applications/NXxas_trans.nxdl.xml @@ -21,7 +21,7 @@ # # For further information, see http://www.nexusformat.org --> - @@ -78,5 +78,33 @@ + + + The spacing between crystal planes of the reflection (e.g., in + Angstroms). Optional but important as it allows to recalibrate + the energy axis from the angle of the monochromator. + + + + + + The spacing between crystal planes of the reflection + + + + + + + + + + + + + + + + + From 2c17cbd9ff8249b75bb2919c43ee7aa1e633f064 Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Mon, 23 Feb 2026 13:21:07 +0100 Subject: [PATCH 6/7] Clean the base class --- applications/NXxas_new.nxdl.xml | 85 +++------------------------------ 1 file changed, 7 insertions(+), 78 deletions(-) diff --git a/applications/NXxas_new.nxdl.xml b/applications/NXxas_new.nxdl.xml index f9957a463e..1892b7720f 100644 --- a/applications/NXxas_new.nxdl.xml +++ b/applications/NXxas_new.nxdl.xml @@ -3,7 +3,7 @@