MODULE obs_sequence_mod

Overview

Provides interfaces to the observation type and observation sequence type. An observation contains everything there is to know about an observation including all metadata contained in the observation definition and any number of copies of data associated with the observation (for instance an actual observation, an ensemble of first guess values, etc). An observation sequence is a time-ordered set of observations that is defined by a linked list so that observations can be easily added or deleted. A number of commands to extract observations depending on the times at which they were taken are provided. For now, the observations are only ordered by time, but the ability to add extra sort keys could be added.

These routines are commonly used in conversion programs which read observation data from various formats and create a DART observation sequence in memory, and then write it out to a file. See the observations directory for examples of programs which create and manipulate observations using this routines.

Other modules used

types_mod
location_mod (depends on model_choice)
obs_def_mod
time_manager_mod
utilities_mod
obs_kind_mod

Public interfaces

use obs_sequence_mod, only :	obs_sequence_type
	init_obs_sequence
	interactive_obs_sequence
	get_num_copies
	get_num_qc
	get_num_obs
	get_max_num_obs
	get_copy_meta_data
	get_qc_meta_data
	get_next_obs
	get_prev_obs
	get_next_obs_from_key
	get_prev_obs_from_key
	insert_obs_in_seq
	delete_obs_from_seq
	set_copy_meta_data
	set_qc_meta_data
	get_first_obs
	get_last_obs
	add_copies
	add_qc
	write_obs_seq
	read_obs_seq
	append_obs_to_seq
	get_obs_from_key
	get_obs_time_range
	set_obs
	get_time_range_keys
	get_num_times
	static_init_obs_sequence
	destroy_obs_sequence
	read_obs_seq_header
	get_expected_obs
	delete_seq_head
	delete_seq_tail
	LINKS BELOW FOR OBS_TYPE INTERFACES
	obs_type
	init_obs
	destroy_obs
	get_obs_def
	set_obs_def
	get_obs_values
	set_obs_values
	replace_obs_values
	get_qc
	set_qc
	replace_qc
	write_obs
	read_obs
	interactive_obs
	copy_obs
	assignment(=)

type obs_sequence_type
   private
   integer                       :: num_copies
   integer                       :: num_qc
   integer                       :: num_obs
   integer                       :: max_num_obs
   character(len=64), pointer    :: copy_meta_data(:)
   character(len=64), pointer    :: qc_meta_data(:)
   integer                       :: first_time
   integer                       :: last_time
   type(obs_type), pointer       :: obs(:)
end type obs_sequence_type

The obs_sequence type represents a series of observations including multiple copies of data and quality control fields and complete metadata about the observations. The sequence is organized as an integer pointer linked list using a fixed array of storage for obs (type obs_type). Each observation points to the previous and next observation in time order (additional sort keys could be added if needed) and has a unique integer key (see obs_type below). The maximum number of observations in the sequence is represented in the type as max_num_obs, the current number of observations is in num_obs. The number of quality control (qc) fields per observation is num_qc and the number of data values associated with each observation is num_copies. Metadata for each copy of the data is in copy_meta_data and metadata for the qc fields is in qc_meta_data. The first and last pointers into the time linked list are in first_time and last_time. A capability to write and read an obs_sequence structure to disk is available. At present, the entire observation sequence is read in to core memory. An on-disk implementation may be necessary for very large observational datasets.

Component	Description
num_copies	Number of data values associated with each observation.
num_qc	Number of qc fields associated with each observation.
num_obs	Number of observations currently in sequence.
max_num_obs	Upper bounds on number of observations in sequence.
copy_meta_data	Text describing each copy of data associated with observations.
qc_meta_data	Text describing each quality control field.
first_time	Location of first observation in sequence.
last_time	Location of last observation in sequence.
obs	Storage for all of the observations in the sequence.

type obs_type
   private
   integer            :: key
   type(obs_def_type) :: def
   real(r8), pointer  :: values(:)
   real(r8), pointer  :: qc(:)
   integer            :: prev_time
   integer            :: next_time
   integer            :: cov_group
end type obs_type

Structure to represent everything known about a given observation and to help with storing the observation in the observation sequence structure (see above). The prev_time and next_time are integer pointers that allow a linked list sorted on time to be constructed. If needed, other sort keys could be introduced (for instance by time available?). Each observation in a sequence has a unique key and each observation has an obs_def_type that contains all the definition and metadata for the observation. A set of values is associated with the observation along with a set of qc fields. The cov_group is not yet implemented but will allow non-diagonal observation error covariances in a future release.

Component	Description
key	Unique integer key when in an obs_sequence.
def	The definition of the observation (see obs_def_mod).
values	Values associated with the observation.
qc	Quality control fields associated with the observation.
prev_time	When in an obs_sequence, points to previous time sorted observation.
next_time	When in an obs_sequence, points to next time sorted observation.
cov_group	Not currently implemented.

call init_obs_sequence(seq, num_copies, num_qc, expected_max_num_obs)

type(obs_sequence_type), intent(out) :: seq
integer,                 intent(in)  :: num_copies
integer,                 intent(in)  :: num_qc
integer,                 intent(in)  :: expected_max_num_obs

Constructor to create a variable of obs_sequence_type. This routine must be called before using an obs_sequence_type. The number of copies of the data to be associated with each observation (for instance the observation from an instrument, an ensemble of prior guesses, etc.) and the number of quality control fields associated with each observation must be specified. Also, an estimated upper bound on the number of observations to be stored in the sequence is helpful in making creation of the sequence efficient.

seq	The observation sequence being constructed
num_copies	Number of copies of data to be associated with each observation
num_qc	Number of quality control fields associated with each observation
expected_max_num_obs	An estimate of the largest number of observations the sequence might contain

var = interactive_obs_sequence()

type(obs_sequence_type) :: interactive_obs_sequence

Uses input from standard in to create an observation sequence. Initialization of the sequence is handled by the function.

var	An observation sequence created from standard input

var = get_num_copies(seq)

integer                             :: get_num_copies
type(obs_sequence_type), intent(in) :: seq

Returns number of copies of data associated with each observation in an observation sequence.

var	Returns number of copies of data associated with each observation in sequence
seq	An observation sequence

var = get_num_qc(seq)

integer                             :: get_num_qc
type(obs_sequence_type), intent(in) :: seq

Returns number of quality control fields associated with each observation in an observation sequence.

var	Returns number of quality control fields associated with each observation in sequence
seq	An observation sequence

var = get_num_obs(seq)

integer                             :: get_num_obs
type(obs_sequence_type), intent(in) :: seq

Returns number of observations currently in an observation sequence.

var	Returns number of observations currently in an observation sequence
seq	An observation sequence

var = get_max_num_obs(seq)

integer                             :: get_max_num_obs
type(obs_sequence_type), intent(in) :: seq

Returns maximum number of observations an observation sequence can hold.

var	Returns maximum number of observations an observation sequence can hold
seq	An observation sequence

var = get_copy_meta_data(seq, copy_num)

character(len=64)                   :: get_copy_meta_data
type(obs_sequence_type), intent(in) :: seq
integer,                 intent(in) :: copy_num

Returns metadata associated with a given copy of data in an observation sequence.

var	Returns metadata associated with a copy of data in observation sequence
seq	An observation sequence
copy_num	Return metadata for this copy

var = get_qc_meta_data(seq,qc_num)

character(len=64)                   :: get_qc_meta_data
type(obs_sequence_type), intent(in) :: seq
integer,                 intent(in) :: qc_num

Returns metadata associated with a given copy of quality control fields associated with observations in an observation sequence.

var	Returns metadata associated with a given qc copy
seq	An observation sequence
qc_num	Return metadata for this copy

call get_next_obs(seq, obs, next_obs, is_this_last)

type(obs_sequence_type), intent(in)  :: seq
type(obs_type),          intent(in)  :: obs
type(obs_type),          intent(out) :: next_obs
logical,                 intent(out) :: is_this_last

Given an observation in a sequence, returns the next observation in the sequence. If there is no next observation, is_this_last is set to true.

seq	An observation sequence
obs	Find the next observation after this one
next_obs	Return the next observation here
is_this_last	True if obs is the last obs in sequence

call get_prev_obs(seq, obs, prev_obs, is_this_first)

type(obs_sequence_type), intent(in)  :: seq
type(obs_type),          intent(in)  :: obs
type(obs_type),          intent(out) :: prev_obs
logical,                 intent(out) :: is_this_first

Given an observation in a sequence, returns the previous observation in the sequence. If there is no previous observation, is_this_first is set to true.

seq	An observation sequence
obs	Find the previous observation before this one
prev_obs	Return the previous observation here
is_this_first	True if obs is the first obs in sequence

call get_next_obs_from_key(seq, last_key_used, next_obs, is_this_last)

type(obs_sequence_type), intent(in)  :: seq
integer,                 intent(in)  :: last_key_used
type(obs_type),          intent(out) :: next_obs
logical,                 intent(out) :: is_this_last

Given the last key used in a sequence, returns the next observation in the sequence. If there is no next observation, is_this_last is set to true.

seq	An observation sequence
last_key_used	Find the next observation after this key
next_obs	Return the next observation here
is_this_last	True if obs is the last obs in sequence

call get_prev_obs_from_key(seq, last_key_used, prev_obs, is_this_first)

type(obs_sequence_type), intent(in)  :: seq
integer,                 intent(in)  :: last_key_used
type(obs_type),          intent(out) :: prev_obs
logical,                 intent(out) :: is_this_first

Given the last key used in a sequence, returns the previous observation in the sequence. If there is no previous observation, is_this_first is set to true.

seq	An observation sequence
last_key_used	Find the previous observation before this key
prev_obs	Return the previous observation here
is_this_first	True if obs is the first obs in sequence

call get_obs_from_key(seq, key, obs)

type(obs_sequence_type), intent(in)  :: seq
integer,                 intent(in)  :: key
type(obs_type),          intent(out) :: obs

Each entry in an observation sequence has a unique integer key. This subroutine returns the observation given an integer key.

seq	An observation sequence
key	Return the observation with this key
obs	The returned observation

call insert_obs_in_seq(seq, obs [, prev_obs])

type(obs_sequence_type),  intent(inout) :: seq
type(obs_type),           intent(inout) :: obs
type(obs_type), optional, intent(in)    :: prev_obs

Inserts an observation in a sequence in appropriate time order. If the optional argument prev_obs is present, the new observation is inserted directly after the prev_obs. If an incorrect prev_obs is provided so that the sequence is no longer time ordered, bad things will happen.

seq	An observation sequence
obs	An observation to be inserted in the sequence
prev_obs	If present, says the new observation belongs immediately after this one

call delete_obs_from_seq(seq, obs)

type(obs_sequence_type), intent(inout) :: seq
type(obs_type),          intent(inout) :: obs

Given an observation and a sequence, removes the observation with the same key from the observation sequence.

seq	An observation sequence
obs	The observation to be deleted from the sequence

call set_copy_meta_data(seq, copy_num, meta_data)

type(obs_sequence_type), intent(inout) :: seq
integer,                 intent(in)    :: copy_num
character(len=64),       intent(in)    :: meta_data

Sets the copy metadata for this copy of the observations in an observation sequence.

seq	An observation sequence
copy_num	Set metadata for this copy of data
meta_data	The metadata

call set_qc_meta_data(seq, qc_num, meta_data)

type(obs_sequence_type), intent(inout) :: seq
integer,                 intent(in)    :: qc_num
character(len=64),       intent(in)    :: meta_data

Sets the quality control metadata for this copy of the qc in an observation sequence.

seq	An observation sequence
qc_num	Set metadata for this quality control field
meta_data	The metadata

var = get_first_obs(seq, obs)

logical                              :: get_first_obs
type(obs_sequence_type), intent(in)  :: seq
type(obs_type),          intent(out) :: obs

Returns the first observation in a sequence. If there are no observations in the sequence, the function returns false, else true.

var	Returns false if there are no obs in sequence
seq	An observation sequence
obs	The first observation in the sequence

var = get_last_obs(seq, obs)

logical                              :: get_last_obs
type(obs_sequence_type), intent(in)  :: seq
type(obs_type),          intent(out) :: obs

Returns the last observation in a sequence. If there are no observations in the sequence, the function returns false, else true.

var	Returns false if there are no obs in sequence
seq	An observation sequence
obs	The last observation in the sequence

call add_copies(seq, num_to_add)

type(obs_sequence_type), intent(inout) :: seq
integer,                 intent(in)    :: num_to_add

Increases the number of copies of data associated with each observation by num_to_add. The current implementation re-creates the entire observation sequence by deallocating and reallocating each entry with a larger size.

seq	An observation sequence
num_to_add	Number of copies of data to add

call add_qc(seq, num_to_add)

type(obs_sequence_type), intent(inout) :: seq
integer,                 intent(in)    :: num_to_add

Increases the number of quality control fields associated with each observation by num_to_add. The current implementation re-creates the entire observation sequence by deallocating and reallocating each entry with a larger size.

seq	An observation sequence
num_to_add	Number of quality control fields to add

call read_obs_seq(file_name, add_copies, add_qc, add_obs, seq)

character(len=*),        intent(in)  :: file_name
integer,                 intent(in)  :: add_copies
integer,                 intent(in)  :: add_qc
integer,                 intent(in)  :: add_obs
type(obs_sequence_type), intent(out) :: seq

Read an observation sequence from file_name. The sequence will have enough space for the number of observations in the file plus any additional space requested by the “add_xx” args. It is more efficient to allocate the additional space at create time rather than try to add it in later. The arguments can specify that the caller wants to add additional data copies associated with each observation, or to add additional quality control fields, or to add space for additional observations. The format of the file (formatted vs. unformatted) has been automatically detected since the I release. The obs_sequence file format with I and later releases has a header that associates observation type strings with an integer which was not present in previous versions. I format files are no longer supported.

file_name	Read from this file
add_copies	Add this number of copies of data to the obs_sequence on file
add_qc	Add this number of qc fields to the obs_sequence on file
add_obs	Add space for this number of additional observations to the obs_sequence on file
seq	The observation sequence read in with any additional space

call write_obs_seq(seq, file_name)

type(obs_sequence_type), intent(in) :: seq
character(len=*),        intent(in) :: file_name

Write the observation sequence to file file_name. The format is controlled by the namelist parameter write_binary_obs_sequence.

seq	An observation sequence
file_name	Write the sequence to this file

call set_obs(seq,obs [, key_in])

type(obs_sequence_type), intent(inout) :: seq
type(obs_type),          intent(in)    :: obs
integer, optional,       intent(in)    :: key_in

Given an observation, copies this observation into the observation sequence using the key specified in the observation. If the optional key_in argument is present, the observation is instead copied into this element of the observation sequence (and the key is changed to be key_in).

seq	An observation sequence
obs	Observation to be put in sequence
key_in	If present, the obs is copied into this key of the sequence

call append_obs_to_seq(seq, obs)

type(obs_sequence_type), intent(inout) :: seq
type(obs_type),          intent(inout) :: obs

Append an observation to an observation sequence. An error results if the time of the observation is not equal to or later than the time of the last observation currently in the sequence.

seq	An observation sequence
obs	Append this observation to the sequence

call get_obs_time_range(seq, time1, time2, key_bounds, num_keys, out_of_range [, obs])

type(obs_sequence_type),  intent(in)  :: seq
type(time_type),          intent(in)  :: time1
type(time_type),          intent(in)  :: time2
integer, dimension(2),    intent(out) :: key_bounds
integer,                  intent(out) :: num_keys
logical,                  intent(out) :: out_of_range
type(obs_type), optional, intent(in)  :: obs

Given a time range specified by a beginning and ending time, find the keys that bound all observations in this time range and the number of observations in the time range. The routine get_time_range_keys can then be used to get a list of all the keys in the range if desired. The logical out_of_range is returned as true if the beginning time of the time range is after the time of the latest observation in the sequence. The optional argument obs can increase the efficiency of the search through the sequence by indicating that all observations before obs are definitely at times before the start of the time range.

seq	An observation sequence
time1	Lower time bound
time2	Upper time bound
key_bounds	Lower and upper bounds on keys that are in the time range
num_keys	Number of keys in the time range
out_of_range	Returns true if the time range is entirely past the time of the last obs in sequence
obs	If present, can start search for time range from this observation

call get_time_range_keys(seq, key_bounds, num_keys, keys)

type(obs_sequence_type),      intent(in)  :: seq
integer, dimension(2),        intent(in)  :: key_bounds
integer,                      intent(in)  :: num_keys
integer, dimension(num_keys), intent(out) :: keys

Given the keys of the observations at the start and end of a time range and the number of observations in the time range (these are returned by get_obs_time_range()), return a list of the keys of all observations in the time range. Combining the two routines allows one to get a list of all observations in any time range by key. The keys array must be at least num_keys long to hold the return values.

seq	An observation sequence
key_bounds	Keys of first and last observation in a time range
num_keys	Number of obs in the time range
keys	Output list of keys of all obs in the time range

var = get_num_times(seq)

integer                             :: get_num_times
type(obs_sequence_type), intent(in) :: seq

Returns the number of unique times associated with observations in an observation sequence.

var	Number of unique times for observations in a sequence
seq	An observation sequence

var = get_num_key_range(seq, key1, key2)

integer                             :: get_num_key_range
type(obs_sequence_type), intent(in) :: seq
integer, optional,       intent(in) :: key1, key2

Returns the number of observations between the two given keys. The default key numbers are the first and last in the sequence file. This routine can be used to count the actual number of observations in a sequence and will be accurate even if the sequence has been trimmed with delete_seq_head() or delete_seq_tail().

var	Number of unique times for observations in a sequence
seq	An observation sequence
key1	The starting key number. Defaults to the first observation in the sequence.
key2	The ending key number. Defaults to the last observation in the sequence.

call static_init_obs_sequence()

Initializes the obs_sequence module and reads namelists. This MUST BE CALLED BEFORE USING ANY OTHER INTERFACES.

call destroy_obs_sequence(seq)

type(obs_sequence_type), intent(inout) :: seq

Releases all allocated storage associated with an observation sequence.

seq	An observation sequence

call read_obs_seq_header(file_name, num_copies, num_qc, num_obs, max_num_obs, file_id, read_format, pre_I_format [, close_the_file])

character(len=*),   intent(in)  :: file_name
integer,            intent(out) :: num_copies
integer,            intent(out) :: num_qc
integer,            intent(out) :: num_obs
integer,            intent(out) :: max_num_obs
integer,            intent(out) :: file_id
character(len=*),   intent(out) :: read_format
logical,            intent(out) :: pre_I_format
logical, optional,  intent(in)  :: close_the_file

Allows one to see the global metadata associated with an observation sequence that has been written to a file without reading the whole file.

file_name	File contatining an obs_sequence
num_copies	Number of copies of data associated with each observation
num_qc	Number of quality control fields associated with each observation
num_obs	Number of observations in sequence
max_num_obs	Maximum number of observations sequence could hold
file_id	File channel/descriptor returned from opening the file
read_format	Either the string 'unformatted' or 'formatted'
pre_I_format	Returns .true. if the file was written before the observation type string/index number table was added to the standard header starting with the I release.
close_the_file	If specified and .TRUE. close the file after the header has been read. The default is to leave the file open.

call init_obs(obs, num_copies, num_qc)

type(obs_type), intent(out) :: obs
integer,        intent(in)  :: num_copies
integer,        intent(in)  :: num_qc

Initializes an obs_type variable. This allocates storage for the observation type and creates the appropriate obs_def_type and related structures. IT IS ESSENTIAL THAT OBS_TYPE VARIABLES BE INITIALIZED BEFORE USE.

obs	An obs_type data structure to be initialized
num_copies	Number of copies of data associated with observation
num_qc	Number of qc fields associated with observation

call destroy_obs(obs)

type(obs_type), intent(inout) :: obs

Destroys an observation variable by releasing all associated storage.

obs	An observation variable to be destroyed

call get_obs_def(obs, obs_def)

type(obs_type),     intent(in)  :: obs
type(obs_def_type), intent(out) :: obs_def

Extracts the definition portion of an observation.

obs	An observation
obs_def	The definition portion of the observation

call set_obs_def(obs, obs_def)

type(obs_type),     intent(out) :: obs
type(obs_def_type), intent(in)  :: obs_def

Given an observation and an observation definition, insert the definition in the observation structure.

obs	An observation whose definition portion will be updated
obs_def	The observation definition that will be inserted in obs

call get_obs_values(obs, values [, copy_indx])

type(obs_type),         intent(in)  :: obs
real(r8), dimension(:), intent(out) :: values
integer, optional,      intent(in)  :: copy_indx

Extract copies of the data from an observation. If copy_indx is present extract a single value indexed by copy_indx into values(1). copy_indx must be between 1 and num_copies, inclusive. If copy_indx is not present extract all copies of data into the values array which must be num_copies long (See get_num_copies.)

obs	Observation from which to extract values
values	The values extracted
copy_indx	If present extract only this copy, otherwise extract all copies

call get_qc(obs, qc [, qc_indx])

type(obs_type),         intent(in)  :: obs
real(r8), dimension(:), intent(out) :: qc
integer, optional,      intent(in)  :: qc_indx

Extract quality control fields from an observation. If qc_indx is present extract a single field indexed by qc_indx into qc(1). qc_indx must be between 1 and num_qc, inclusive. If qc_indx is not present extract all quality control fields into the qc array which must be num_qc long (See get_num_qc.)

obs	Observation from which to extract qc field(s)
qc	Extracted qc fields
qc_indx	If present extract only this field, otherwise extract all qc fields

call set_obs_values(obs, values [, copy_indx])

type(obs_type),         intent(out) :: obs
real(r8), dimension(:), intent(in)  :: values
integer, optional,      intent(in)  :: copy_indx

Set value(s) of data in this observation. If copy_indx is present set the single value indexed by copy_indx to values(1). copy_indx must be between 1 and num_copies, inclusive. If copy_indx is not present set all copies of data from the values array which must be num_copies long (See get_num_copies.)

obs	Observation whose values are being set
values	Array of value(s) to be set
copy_indx	If present set only this copy of data, otherwise set all copies

call replace_obs_values(seq, key, values [, copy_indx])

type(obs_sequence_type), intent(inout) :: seq
integer,                 intent(in)    :: key
real(r8), dimension(:),  intent(in)    :: values
integer, optional,       intent(in)    :: copy_indx

Set value(s) of data in the observation from a sequence with the given key. If copy_indx is present set the single value indexed by copy_indx to values(1). copy_indx must be between 1 and num_copies, inclusive. If copy_indx is not present set all copies of data from the values array which must be num_copies long (See get_num_copies.)

seq	Sequence which contains observation to update
key	Key to select which observation
values	Array of value(s) to be set
copy_indx	If present set only this copy of data, otherwise set all copies

call set_qc(obs, qc [, qc_indx])

type(obs_type),         intent(out) :: obs
real(r8), dimension(:), intent(in)  :: qc
integer, optional,      intent(in)  :: qc_indx

Sets the quality control fields in an observation. If qc_indx is present set a single field indexed by qc_indx to qc(1). qc_indx must be between 1 and num_qc, inclusive. If qc_indx is not present set all quality control fields from the qc array which must be num_qc long (See get_num_qc.)

obs	Observation having its qc fields set
qc	Input values of qc fields
qc_indx	If present update only this field, otherwise update all qc fields

call replace_qc(seq, key, qc [, qc_indx])

type(obs_sequence_type), intent(inout) :: seq
integer,                 intent(in)    :: key
real(r8), dimension(:),  intent(in)    :: qc
integer, optional,       intent(in)    :: qc_indx

Set value(s) of the quality control fields in the observation from a sequence with the given key. If qc_indx is present set the single value indexed by qc_indx to qc(1). qc_indx must be between 1 and num_qc, inclusive. If qc_indx is not present set all quality control fields from the qc array which must be num_qc long (See get_num_qc.)

seq	Observation sequence containing observation to update
key	Key to select which observation
qc	Input values of qc fields
qc_indx	If present, only update single qc field, else update all qc fields

call write_obs(obs, file_id, num_copies, num_qc)

type(obs_type), intent(in) :: obs
integer,        intent(in) :: file_id
integer,        intent(in) :: num_copies
integer,        intent(in) :: num_qc

Writes an observation and all its associated metadata to a disk file that has been opened with a format consistent with the namelist parameter write_binary_obs_sequence.

obs	Observation to be written to file
file_id	Channel open to file for writing
num_copies	The number of copies of data associated with the observation to be output
num_qc	The number of qc fields associated with the observation to be output

call read_obs(file_id, num_copies, add_copies, num_qc, add_qc, key, obs, read_format [, max_obs])

integer,            intent(in)    :: file_id
integer,            intent(in)    :: num_copies
integer,            intent(in)    :: add_copies
integer,            intent(in)    :: num_qc
integer,            intent(in)    :: add_qc
integer,            intent(in)    :: key
type(obs_type),     intent(inout) :: obs
character(len=*),   intent(in)    :: read_format
integer, optional,  intent(in)    :: max_obs

Reads an observation from an obs_sequence file. The number of copies of data and the number of qc values associated with each observation must be provided. If additional copies of data or additional qc fields are needed, arguments allow them to be added. WARNING: The key argument is no longer used and should be removed.

file_id	Channel open to file from which to read
num_copies	Number of copies of data associated with observation in file
add_copies	Number of additional copies of observation to be added
num_qc	Number of qc fields associated with observation in file
add_qc	Number of additional qc fields to be added
key	No longer used, should be deleted
obs	The observation being read in
read_format	Either the string 'formatted' or 'unformatted'
max_obs	If present, specifies the largest observation key number in the sequence. This is used only for additional error checks on the next and previous obs linked list values.

call interactive_obs(num_copies, num_qc, obs, key)

integer,        intent(in)    :: num_copies
integer,        intent(in)    :: num_qc
type(obs_type), intent(inout) :: obs
integer,        intent(in)    :: key

Use standard input to create an observation. The number of values, number of qc fields, and an observation type-specific key associated with the observation are input. (Note that the key here is not the same as the key in an observation sequence.)

num_copies	Number of copies of data to be associated with observation
num_qc	Number of qc fields to be associated with observation
obs	Observation created via standard input
key	An observation type-specific key can be associated with each observation for use by the obs_def code.

call copy_obs(obs1, obs2)

type(obs_type), intent(out) :: obs1
type(obs_type), intent(in)  :: obs2

Copies the observation type obs2 to obs1. If the sizes of obs fields are not compatible, the space in obs1 is deallocated and reallocated with the appropriate size. This is overloaded to assignment(=).

obs1	Copy obs2 to here (destination)
obs2	Copy into obs1 (source)

call get_expected_obs_from_def_distrib_state(state_handle, ens_size, copy_indices, key, & obs_def, obs_kind_ind, state_time, isprior, assimilate_this_ob, evaluate_this_ob, expected_obs, & istatus)

type(ensemble_type), intent(in)  :: state_handle
integer,             intent(in)  :: ens_size
integer,             intent(in)  :: copy_indices(ens_size)
integer,             intent(in)  :: key
type(obs_def_type),  intent(in)  :: obs_def
integer,             intent(in)  :: obs_kind_ind
type(time_type),     intent(in)  :: state_time
logical,             intent(in)  :: isprior
integer,             intent(out) :: istatus(ens_size)
logical,             intent(out) :: assimilate_this_ob, evaluate_this_ob
real(r8),            intent(out) :: expected_obs(ens_size)

Used to compute the expected value of a set of observations in an observation sequence given a model state vector. Also returns a status variable that reports on problems taking forward operators. This version returns forward operator values for the entire ensemble in a single call.

state_handle	An observation sequence
keys	List of integer keys that specify observations in seq
ens_index	The ensemble number for this state vector
state	Model state vector
state_time	The time of the state data
obs_vals	Returned expected values of the observations
istatus	Integer error code for use in quality control (0 means no error)
assimilate_this_ob	Returns true if this observation type is being assimilated
evaluate_this_ob	Returns true if this observation type is being evaluated but not assimilated

call delete_seq_head(first_time, seq, all_gone)

type(time_type),         intent(in)    :: first_time
type(obs_sequence_type), intent(inout) :: seq
logical,                 intent(out)   :: all_gone

Deletes all observations in the sequence with times before first_time. If no observations remain, return all_gone as .true. If no observations fall into the time window (e.g. all before first_time or empty sequence to begin with), no deletions are done and all_gone is simply returned as .true.

first_time	Delete all observations with times before this
seq	An observation sequence
all_gone	Returns true if there are no valid observations remaining in the sequence after first_time

call delete_seq_tail(last_time, seq, all_gone)

type(time_type),         intent(in)    :: last_time
type(obs_sequence_type), intent(inout) :: seq
logical,                 intent(out)   :: all_gone

Deletes all observations in the sequence with times after last_time. If no observations remain, return all_gone as .true. If no observations fall into the time window (e.g. all after last_time or empty sequence to begin with), no deletions are done and all_gone is simply returned as .true.

last_time	Delete all observations with times after this
seq	An observation sequence
all_gone	Returns true if there are no valid observations remaining in the sequence before last_time

Namelist

This namelist is read from the file input.nml. Namelists start with an ampersand ‘&’ and terminate with a slash ‘/’. Character strings that contain a ‘/’ must be enclosed in quotes to prevent them from prematurely terminating the namelist.

&obs_sequence_nml
   write_binary_obs_sequence = .false.
   read_binary_file_format   = 'native'
  /

Item	Type	Description
write_binary_obs_sequence	logical	If true, write binary obs_sequence files. If false, write ascii obs_sequence files.
read_binary_file_format	character(len=32)	The ‘endian’ness of binary obs_sequence files. May be ‘native’ (endianness matches hardware default), ‘big-endian’, ‘little-endian’, and possibly ‘cray’. Ignored if observation sequence files are ASCII.

Files

• obs_sequence_mod.nml in input.nml

• Files for reading and writing obs_sequences and obs specified in filter_nml.

References

• none

Private components

N/A