From aee3827402f3d67b05b559eaf96d0835a74ad594 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:26:20 -0600 Subject: [PATCH 01/16] Replace 'dataset' with 'field' Data sets can mean a multitude of things in different contexts. For example, in many data catalogs, data sets refer to collections of data objects. Even within this file, some might construe 'dataset' to refer to the plottable data. However, there are many uses of the word 'field', which is less ambiguous, so I would propose that this is used wherever we are referring to an item in the group. --- base_classes/NXdata.nxdl.xml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 8e6a3f2ff0..bdd6d95f57 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -42,9 +42,9 @@ --> - These symbols will be used below to coordinate datasets with the same shape. rank of the ``data`` field length of the ``variable`` field + These symbols will be used below to coordinate fields with the same shape. length of the ``x`` field length of the ``y`` field length of the ``z`` field @@ -54,13 +54,13 @@ .. index:: plotting - Declares which dataset is the default. - The value is the name of the dataset to be plotted. - A field of this name *must* exist (either as dataset - or as a link to a dataset). + Declares which field contains the default plottable data. + The value is the name of the field to be plotted. + A field of this name *must* exist (either as field + or as a link to a field in another group). It is recommended (as of NIAC2014) to use this attribute - rather than adding a signal attribute to the dataset. + rather than adding a signal attribute to the field. See http://wiki.nexusformat.org/2014_How_to_find_default_data for a summary of the discussion. @@ -163,10 +163,10 @@ to provide a default plot for the data of this :ref:`NXentry`. The actual data might be stored in another group and (hard) linked to the :ref:`NXdata` group. - * Each :ref:`NXdata` group will define only one data set - containing plottable data, dimension scales, and - possibly associated standard deviations. - Other data sets may be present in the group. + * Each :ref:`NXdata` group will define only one field + containing plottable data, one for each of the dimension scales, and, + optionally, associated uncertainties. Other fields may be present in + the group. * The plottable data may be of arbitrary rank up to a maximum of ``NX_MAXRANK=32``. * The plottable data will be named as the value of @@ -180,7 +180,7 @@ mr: float[100] --> the default independent data The field named in the ``signal`` attribute **must** exist, either - directly as a dataset or defined through a link. + directly as a field or defined through a link. * The group ``axes`` attribute will name the *dimension scale* associated with the plottable data. @@ -200,7 +200,7 @@ The preferred method to associate each data dimension with its respective dimension scale is to specify the field name of each dimension scale in the group ``axes`` attribute as a string list. - Here is an example for a 2-D data set *data* plotted + Here is an example for 2-D data, *data*, plotted against *time*, and *pressure*. (An additional *temperature* data set is provided and could be selected as an alternate for the *pressure* axis.):: From 619d077032590f4f261d2fd05dbea5680469d0e9 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:32:10 -0600 Subject: [PATCH 02/16] Rename VARIABLE and AXISNAME The use of 'VARIABLE' was presumably inspired by the term 'independent variable', but this is scarcely used in favor of 'dimension scale'. Since we are always referring to an axis, I suggest changing 'VARIABLE' to 'AXIS'. Since both refer to an arbitrary name, the use of 'AXISNAME' is redundant. I also made a couple of references upper case for consistency. --- base_classes/NXdata.nxdl.xml | 45 +++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index bdd6d95f57..e57f220f26 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -42,9 +42,9 @@ --> - rank of the ``data`` field - length of the ``variable`` field These symbols will be used below to coordinate fields with the same shape. + rank of the ``DATA`` field + length of the ``AXIS`` field length of the ``x`` field length of the ``y`` field length of the ``z`` field @@ -76,10 +76,9 @@ the ``signal`` attribute of this group). One entry is provided for every dimension in the *signal* field. - The field(s) named as values (known as "axes") of this attribute - *must* exist. An axis slice is specified using a field named - ``AXISNAME_indices`` as described below (where the text shown here - as ``AXISNAME`` is to be replaced by the actual field name). + An axis slice is specified using a field named + ``AXIS_indices`` as described below (where the text shown here + as ``AXIS`` is to be replaced by the actual field name). When no default axis is available for a particular dimension of the plottable data, use a "." in that position. @@ -99,26 +98,26 @@ the axes attribute can be omitted. - + - + - Each ``AXISNAME_indices`` attribute indicates the dependency - relationship of the ``AXISNAME`` field (where ``AXISNAME`` + Each ``AXIS_indices`` attribute indicates the dependency + relationship of the ``AXIS`` field (where ``AXIS`` is the name of a field that exists in this ``NXdata`` group) with one or more dimensions of the plottable data. Integer array that defines the indices of the *signal* field (that field will be a multidimensional array) - which need to be used in the *AXISNAME* dataset in + which need to be used in the *AXIS* field in order to reference the corresponding axis value. The first index of an array is ``0`` (zero). - Here, *AXISNAME* is to be replaced by the name of each + Here, *AXIS* is to be replaced by the name of each field described in the ``axes`` attribute. An example with 2-D data, :math:`d(t,P)`, will illustrate:: @@ -160,8 +159,12 @@ are plottable data and which are *dimension scales*, respectively. :ref:`NXdata` is used to implement one of the basic motivations in NeXus, - to provide a default plot for the data of this :ref:`NXentry`. The actual data - might be stored in another group and (hard) linked to the :ref:`NXdata` group. + to identify plottable data in each :ref:`NXentry`. The actual data + might be stored in another group and linked to the :ref:`NXdata` group. + + ..note:: Note that, in the following, ``DATA`` and ``AXIS`` + represent the names of fields containing the plottable data and + axes, respectively. The names are not fixed by the standard. * Each :ref:`NXdata` group will define only one field containing plottable data, one for each of the dimension scales, and, @@ -231,7 +234,7 @@ *dimension scale* to identify with an integer the axis whose value is the number of the dimension. - + Dimension scale defining an axis of the data. Client is responsible for defining the dimensions of the data. @@ -265,18 +268,18 @@ - + - Errors (uncertainties) associated with axis ``VARIABLE``. + Errors (uncertainties) associated with axis ``AXIS``. Client is responsible for defining the dimensions of the data. The name of this field may be changed to fit the circumstances - but is matched with the *VARIABLE* + but is matched with the *AXIS* field with ``_errors`` appended. A dimension scale must have a rank of 1 and has length ``n``, - same as ``variable``. + same as ``AXIS``. @@ -360,8 +363,8 @@ The ``errors`` must have the same rank (``dataRank``) - as the ``data``. - At least one ``dim`` must have length "n". + as the ``DATA``. + At least one ``dim`` must have length ``n``. From 7a0493c5f202737996332fbaeba892643a513e3b Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:35:21 -0600 Subject: [PATCH 03/16] Removed redundant fields The 'x', 'y', and 'z fields seem to be specific names for the 'AXIS' fields. I'm not sure why these should be included and not a hundred other possible fields. --- base_classes/NXdata.nxdl.xml | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index e57f220f26..c486732d90 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -45,9 +45,6 @@ These symbols will be used below to coordinate fields with the same shape. rank of the ``DATA`` field length of the ``AXIS`` field - length of the ``x`` field - length of the ``y`` field - length of the ``z`` field @@ -383,32 +380,5 @@ An optional offset to apply to the values in data. - - - This is an array holding the values to use for the x-axis of - data. The units must be appropriate for the measurement. - - - - - - - - This is an array holding the values to use for the y-axis of - data. The units must be appropriate for the measurement. - - - - - - - - This is an array holding the values to use for the z-axis of - data. The units must be appropriate for the measurement. - - - - - From b91e4d7849416bc0b30b14dcd1c4bfadf2682de2 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:41:41 -0600 Subject: [PATCH 04/16] Removed redundant text I object to the phrase "file readers are encouraged to make their best efforts to plot the data" since it implies that the axis definitions become ambiguous. Since I have implemented a generic plotter that has never had a problem in identifying axes unambiguously, I know this is not true. I would suggest that the whole text is unnecessary, and will just confuse any outsiders not familiar with the controversy. All that is needed is a statement that the attributes should be provided, assuming that is still the NIAC recommendation. --- base_classes/NXdata.nxdl.xml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index c486732d90..c9a4af69a3 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -127,14 +127,7 @@ time: float[1000] pressure: float[20] - This attribute is to be provided in all situations. - However, if the indices attributes are missing - (such as for data files written before this specification), - file readers are encouraged to make their best efforts - to plot the data. - Thus the implementation of the - ``AXISNAME_indices`` attribute is based on the model of - "strict writer, liberal reader". + This attribute should be provided in all situations. .. note:: Attributes potentially containing multiple values (axes and _indices) are to be written as string or integer arrays, From 0dec12d7f4ae7a03bdda57ddf635389f0ea3742a Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:42:49 -0600 Subject: [PATCH 05/16] Changed 'mandatory' to 'recommended' It is my understanding that we agreed that the requirement for at least one NXdata group was not mandatory, but strongly encouraged. --- base_classes/NXdata.nxdl.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index c9a4af69a3..5e381904c4 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -140,7 +140,7 @@ .. index:: plotting - It is mandatory that there is at least one :ref:`NXdata` group + It is recommended that there is at least one :ref:`NXdata` group in each :ref:`NXentry` group. Note that the ``variable`` and ``data`` can be defined with different names. From 088ef4f8a4a6570c41583b7a11327e7532e93963 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:46:00 -0600 Subject: [PATCH 06/16] Update definition of uncertainties The current version still assumes that the signal array has an associated array called 'errors', rather than 'DATA_errors' or by using the 'uncertainties' attributes. The changes add these other options, and define 'DATA_errors' - at the moment, only 'AXIS_errors' is defined. --- base_classes/NXdata.nxdl.xml | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 5e381904c4..a44539cf06 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -178,8 +178,10 @@ * The group ``axes`` attribute will name the *dimension scale* associated with the plottable data. - If available, the standard deviations of the data are to be - stored in a data set of the same rank and dimensions, with the name ``errors``. + * If available, the standard deviations of the data are to be + stored in a field of the same rank and dimensions, either with the + name ``DATA_errors`` or with a name specified in the data's + ``uncertainties`` attribute. * For each data dimension, there should be a one-dimensional array of the same length. @@ -342,6 +344,21 @@ data label + + + Errors (uncertainties) associated with data ``DATA``. + Client is responsible for defining the dimensions of the data. + The name of this field may be changed to fit the circumstances + but is matched with the *DATA* + field with ``_errors`` appended. + + + + The dimensions should match those of ``DATA``. + + + + Standard deviations of data values - From c0a593d93e7114948da84954ff5c115512063ccc Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:48:50 -0600 Subject: [PATCH 07/16] Add use of bin boundaries The dimension scale could have a size of one greater than the corresponding signal array if the values are bin boundaries of a data histogram. --- base_classes/NXdata.nxdl.xml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index a44539cf06..a67bc98c4d 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -183,11 +183,12 @@ name ``DATA_errors`` or with a name specified in the data's ``uncertainties`` attribute. - * For each data dimension, there should be a one-dimensional array - of the same length. - * These one-dimensional arrays are the *dimension scales* of the - data, *i.e*. the values of the independent variables at which the data - is measured, such as scattering angle or energy transfer. + * For each data dimension of size ``n``, there should be a + one-dimensional array of size ``n`` or ``n+1``, which contain the + *dimension scales* of the data, *i.e*., the values of the independent + variables at which the data is measured, such as scattering angle or + energy transfer (size ``n``) or the bin boundaries when the data is + histogrammed (size ``n+1 ``). .. index:: link .. index:: axes (attribute) @@ -236,7 +237,8 @@ - A *dimension scale* must have a rank of 1 and has length ``n``. + A *dimension scale* must have a rank of 1 and has length ``n`` + or ``n+1``. From b81ae69ccf4af5ed8fb36e7531f0e82d9ed8f114 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Mon, 27 Nov 2017 16:54:34 -0600 Subject: [PATCH 08/16] Miscellaneous edits The remaining changes are my attempt at improving the understandability of some of the descriptions. I don't think they change the meaning substantively, although I shorten some of the deprecation warnings to make them, I believe, less confusing to the newcomer. --- base_classes/NXdata.nxdl.xml | 78 ++++++++++++++++++++---------------- 1 file changed, 43 insertions(+), 35 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index a67bc98c4d..b2c4d4d1a4 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -67,11 +67,10 @@ .. index:: plotting - String array that defines the independent data fields used in - the default plot for all of the dimensions of the *signal* field - (the *signal* field is the field in this group that is named by - the ``signal`` attribute of this group). + String array that defines the names of independent data fields used + in the default plot for each of the dimensions of the *signal* field. One entry is provided for every dimension in the *signal* field. + The field(s) named in this attribute *must* exist. An axis slice is specified using a field named ``AXIS_indices`` as described below (where the text shown here @@ -83,10 +82,13 @@ @axes="time", ".", "." - Since there are three items in the list, the the *signal* field - must must be a three-dimensional array (rank=3). The first dimension - is described by the values of a one-dimensional array named ``time`` - while the other two dimensions have no fields to be used as dimension scales. + In this example, since there are three items in the list, the + *signal* field must must be a three-dimensional array (rank=3). The + first dimension is described by the values of a one-dimensional + array named ``time`` while the other two dimensions have no fields + to be used as dimension scales. If the dimension scale does not + exist, it is assumed the data will be plotted against the + corresponding array index. See examples provided on the NeXus wiki: http://wiki.nexusformat.org/2014_axes_and_uncertainties @@ -116,6 +118,7 @@ Here, *AXIS* is to be replaced by the name of each field described in the ``axes`` attribute. + An example with 2-D data, :math:`d(t,P)`, will illustrate:: data_2d:NXdata @@ -142,11 +145,9 @@ It is recommended that there is at least one :ref:`NXdata` group in each :ref:`NXentry` group. - Note that the ``variable`` and ``data`` - can be defined with different names. - The ``signal`` and ``axes`` attributes of the - ``data`` group define which items - are plottable data and which are *dimension scales*, respectively. + The ``signal`` and ``axes`` attributes of the ``data`` group define + which fields are plottable data and which are the independent variables, + or *dimension scales*, respectively. :ref:`NXdata` is used to implement one of the basic motivations in NeXus, to identify plottable data in each :ref:`NXentry`. The actual data @@ -162,7 +163,7 @@ the group. * The plottable data may be of arbitrary rank up to a maximum of ``NX_MAXRANK=32``. - * The plottable data will be named as the value of + * The name of the plottable data will be defined by the value of the group ``signal`` attribute, such as:: data:NXdata @@ -175,9 +176,6 @@ The field named in the ``signal`` attribute **must** exist, either directly as a field or defined through a link. - * The group ``axes`` attribute will name the - *dimension scale* associated with the plottable data. - * If available, the standard deviations of the data are to be stored in a field of the same rank and dimensions, either with the name ``DATA_errors`` or with a name specified in the data's @@ -192,13 +190,19 @@ .. index:: link .. index:: axes (attribute) + + * The group ``axes`` attribute will list these *dimension scales*. + associated with the plottable data in the order of their respective + dimension, *i.e.*, starting with the slowest-changing dimension in + row major order. The preferred method to associate each data dimension with its respective dimension scale is to specify the field name of each dimension scale in the group ``axes`` attribute as a string list. Here is an example for 2-D data, *data*, plotted against *time*, and *pressure*. (An additional *temperature* data set - is provided and could be selected as an alternate for the *pressure* axis.):: + is provided and could be selected as an alternate for the *pressure* + axis.):: data_2d:NXdata @signal="data" @@ -215,21 +219,23 @@ There are two older methods of associating each data dimension to its respective dimension scale. - Both are now out of date and - should not be used when writing new data files. - However, client software should expect to see data files + Both should not be used when writing new data files, but + client software should expect to see legacy data files written with any of these methods. - * One method uses the ``axes`` - attribute to specify the names of each *dimension scale*. + * One method adds the ``axes`` attribute to the data, rather than to + the group. This is not recommended because the data field could be + linked from another group, which does not contain all the + *dimension scales*. - * The oldest method uses the ``axis`` attribute on each - *dimension scale* to identify - with an integer the axis whose value is the number of the dimension. + * The oldest method adds am ``axis`` attribute to each + *dimension scale* set to an integer corresponding to the + corresponding dimension. - Dimension scale defining an axis of the data. + Dimension scale defining an axis of the data. There should be one + of these for each dimensions of the ``DATA`` field. Client is responsible for defining the dimensions of the data. The name of this field may be changed to fit the circumstances. Standard NeXus client tools will use the attributes to determine @@ -256,9 +262,8 @@ Index (positive integer) identifying this specific set of numbers. - N.B. The ``axis`` attribute is the old way of designating a link. - Do not use the ``axes`` attribute with the ``axis`` attribute. - The ``axes`` *group* attribute is now preferred. + N.B. The ``axis`` attribute is now deprecated and should not be + used in writing new files. @@ -302,10 +307,13 @@ .. index:: plotting - Plottable (independent) axis, indicate index number. + Plottable (independent) axis, with a value designating its + priority in the :ref:`NXdata` group. Only one field in a :ref:`NXdata` group may have the ``signal=1`` attribute. - Do not use the ``signal`` attribute with the ``axis`` attribute. + + N.B. The ``signal`` attribute is now deprecated + and should not be used in writing new files. From 59e55a4797e6aa98681dd513f016347c9981dad3 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Tue, 30 Jan 2018 08:18:13 -0600 Subject: [PATCH 09/16] Fix indentation --- base_classes/NXdata.nxdl.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index b2c4d4d1a4..6649da5376 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -70,7 +70,7 @@ String array that defines the names of independent data fields used in the default plot for each of the dimensions of the *signal* field. One entry is provided for every dimension in the *signal* field. - The field(s) named in this attribute *must* exist. + The field(s) named in this attribute *must* exist. An axis slice is specified using a field named ``AXIS_indices`` as described below (where the text shown here From 4bac172706fc42202bbd16bd72266e9d174ef0ea Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Tue, 30 Jan 2018 08:27:49 -0600 Subject: [PATCH 10/16] Fix typos and improve wording --- base_classes/NXdata.nxdl.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 6649da5376..fac4394cd9 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -219,8 +219,8 @@ There are two older methods of associating each data dimension to its respective dimension scale. - Both should not be used when writing new data files, but - client software should expect to see legacy data files + Neither should be used when writing new data files, but + client software should expect to see legacy data files written with any of these methods. * One method adds the ``axes`` attribute to the data, rather than to @@ -228,14 +228,14 @@ linked from another group, which does not contain all the *dimension scales*. - * The oldest method adds am ``axis`` attribute to each + * The oldest method adds an ``axis`` attribute to each *dimension scale* set to an integer corresponding to the corresponding dimension. Dimension scale defining an axis of the data. There should be one - of these for each dimensions of the ``DATA`` field. + of these for each dimension of the ``DATA`` field. Client is responsible for defining the dimensions of the data. The name of this field may be changed to fit the circumstances. Standard NeXus client tools will use the attributes to determine From 4c21ea80209280a84eba105ea6ca5f5bdbc05594 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Tue, 30 Jan 2018 08:30:52 -0600 Subject: [PATCH 11/16] Amend wording about uncertainties I have changed it to show that naming the field this way is no longer the recommended way of identifying the uncertainties, but is still a valid naming pattern. --- base_classes/NXdata.nxdl.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index fac4394cd9..bcf7b6b96d 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -356,11 +356,14 @@ - Errors (uncertainties) associated with data ``DATA``. + Errors (uncertainties) associated with data ``DATA``. It is now + recommended that uncertainties are defined using the + ``uncertainties`` attribute of the signal field. The name of this + field does not therefore have to conform to this pattern, i.e., + the name of the signal field with ``_errors`` appended. However, + it does make the association of the two fields clear. Client is responsible for defining the dimensions of the data. - The name of this field may be changed to fit the circumstances - but is matched with the *DATA* - field with ``_errors`` appended. + From 6b9413bbf19d54ef27dce4cca8b4c889d06a6cec Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Tue, 30 Jan 2018 09:37:29 -0600 Subject: [PATCH 12/16] Fix indentation --- base_classes/NXdata.nxdl.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index bcf7b6b96d..feda4e264d 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -153,9 +153,9 @@ to identify plottable data in each :ref:`NXentry`. The actual data might be stored in another group and linked to the :ref:`NXdata` group. - ..note:: Note that, in the following, ``DATA`` and ``AXIS`` - represent the names of fields containing the plottable data and - axes, respectively. The names are not fixed by the standard. + ..note :: Note that, in the following, ``DATA`` and ``AXIS`` + represent the names of fields containing the plottable data and + axes, respectively. The names are not fixed by the standard. * Each :ref:`NXdata` group will define only one field containing plottable data, one for each of the dimension scales, and, From 6ce74b0ca5c195113786424212e6e68b4b58ce27 Mon Sep 17 00:00:00 2001 From: Pete R Jemian Date: Mon, 19 Sep 2022 01:17:40 -0500 Subject: [PATCH 13/16] DOC #602 reST syntax --- base_classes/NXdata.nxdl.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 0b2844a5ae..621c0c2593 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -194,10 +194,10 @@ * For each data dimension of size ``n``, there should be a one-dimensional array of size ``n`` or ``n+1``, which contain the - *dimension scales* of the data, *i.e*., the values of the independent + *dimension scales* of the data, *i.e.*, the values of the independent variables at which the data is measured, such as scattering angle or energy transfer (size ``n``) or the bin boundaries when the data is - histogrammed (size ``n+1 ``). + histogrammed (size ``n+1``). .. index:: link .. index:: axes (attribute) From 4f7e06d2c65073f075328fd07f9a241e06e76193 Mon Sep 17 00:00:00 2001 From: Pete Jemian Date: Mon, 19 Sep 2022 06:24:39 -0500 Subject: [PATCH 14/16] DOC #602 indentation --- base_classes/NXdata.nxdl.xml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 4f91bf3ac8..09dd1ae81a 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -373,8 +373,9 @@ Errors (uncertainties) associated with data ``DATA``. It is now recommended that uncertainties are defined using the ``uncertainties`` attribute of the signal field. - TO provide consistent naming within NeXus, it is recommended the name of this - field do conform to this pattern, i.e., + + To provide consistent naming within NeXus, it is recommended + the name of this field conform to this pattern, i.e., the name of the signal field with ``_errors`` appended. Client is responsible for defining the dimensions of the data. From 9e1b035307464943a0cd1e64d7c4e8d764ce6f48 Mon Sep 17 00:00:00 2001 From: Pete Jemian Date: Mon, 19 Sep 2022 06:29:22 -0500 Subject: [PATCH 15/16] CI #602 spelling --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 05ce33b182..2282909a7a 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -67,7 +67,7 @@ jobs: run: | make prepare - - name: Build Impatient Guid + - name: Build Impatient Guide run: | make impatient-guide ls -lAFgh build/impatient-guide/build/html/index.html From 5c37cbbbc79a16480bc269e09baabba640d5cdac Mon Sep 17 00:00:00 2001 From: Pete Jemian Date: Mon, 19 Sep 2022 06:47:45 -0500 Subject: [PATCH 16/16] DOC #602 AXISNAME -> AXIS per commit 619d077 --- base_classes/NXdata.nxdl.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 09dd1ae81a..072962eeef 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -43,7 +43,7 @@ These symbols will be used below to coordinate fields with the same shape. rank of the ``DATA`` field - length of the ``AXISNAME`` field + length of the ``AXIS`` field length of the ``x`` field length of the ``y`` field length of the ``z`` field @@ -113,7 +113,7 @@ the axes attribute can be omitted. - +