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MODULE obs_sequence_mod

Contact: Jeff Anderson
Revision: $Revision: 2801 $
Source: $URL: http://subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_sequence_mod.html $
Change Date: $Date: 2007-04-04 22:11:48 -0600 (Wed, 04 Apr 2007) $
Change history: try "svn log" or "svn diff"

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 contained in 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.




OTHER MODULES USED

types_mod
location_mod (depends on model_choice)
obs_def_mod
time_manager_mod
utilities_mod
obs_kind_mod



PUBLIC INTERFACE

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(=)

NOTES

Optional namelist interface &obs_sequence_nml may be read from file input.nml.




PUBLIC COMPONENTS





type obs_sequence_type
   private
   integer                       :: num_copies
   integer                       :: num_qc
   integer                       :: num_obs
   integer                       :: max_num_obs
   character(len = 129), pointer :: copy_meta_data(:)
   character(len = 129), pointer :: qc_meta_data(:)
   integer                       :: first_time
   integer                       :: last_time
   type(obs_type), pointer       :: obs(:)
end type obs_sequence_type

Description

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

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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=129)                  :: get_copy_meta_data
 type(obs_sequence_type), intent(in) :: seq
 integer, intent(in)                 :: copy_num
 

Description

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=129)                  :: get_qc_meta_data
 type(obs_sequence_type), intent(in) :: seq
 integer, intent(in)                 :: qc_num
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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), intent(in), optional   :: prev_obs
 

Description

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
 

Description

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=129), intent(in)         :: meta_data
 

Description

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=129), intent(in)         :: meta_data
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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=129), 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
 

Description

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 kind strings with an integer which was not present in previous versions. The default definitions from earlier releases are assumed when an old format sequence file is detected.

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=129), intent(in)      :: file_name
 

Description

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
 

Description

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
 

Description

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), intent(in), optional :: obs
 

Description

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
 

Description

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
 

Description

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


call static_init_obs_sequence()
 

Description

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
 

Description

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=129), 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=129), intent(out) :: read_format
 logical, intent(out)            :: pre_I_format
 logical, intent(in), optional   :: close_the_file
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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
 

Description

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=129), intent(in) :: read_format
 integer, intent(in), optional  :: max_obs
 

Description

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
 

Description

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
 

Description

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(seq, keys, state, obs_vals, istatus, assimilate_this_ob, evaluate_this_ob)
 type(obs_sequence_type), intent(in) :: seq
 integer, dimension(:), intent(in)   :: keys
 real(r8), dimension(:), intent(in)  :: state
 real(r8), dimension(:), intent(out) :: obs_vals
 integer, intent(out)                :: istatus
 logical, intent(out)                :: assimilate_this_ob
 logical, intent(out)                :: evaluate_this_ob
 

Description

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 is normally applied to a single observation at a time but can also be a list for computational efficiency.

seq    An observation sequence
keys    List of integer keys that specify observations in seq
state    Model state vector
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 kind is being assimilated
evaluate_this_ob    Returns true if this observation kind 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
 

Description

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
 

Description

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

We adhere to the F90 standard of starting a namelist with an ampersand '&' and terminating with a slash '/'.

 namelist / obs_sequence_nml /  &
 write_binary_obs_sequence 
 

Discussion

Namelist option control format for output. Note that the write format is used for intermediate files when any of the shell driven options for parallelization are used.

This namelist is read in a file called input.nml

Contents Type Description
write_binary_obs_sequence logical If true, write binary obs_sequence files. Default: false




FILES




REFERENCES


ERROR CODES and CONDITIONS

RoutineMessageComment
insert_obs_in_seq ran out of room, num_obs # > max_num_obs # Overflowed number of obs in sequence. Called from many public entries.
append_obs_to_seq tried to append an obs to sequence with bad time Tried to append an obs with earlier time than last obs in sequence.
append_obs_to_seq ran out of room, max_num_obs = # Overflowed the obs sequence.



KNOWN BUGS




FUTURE PLANS

Future versions should automate file reading and only the write namelist parameter should remain.




PRIVATE COMPONENTS