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IRootLab
An Open-Source MATLAB toolbox for vibrational biospectroscopy
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IRootLab
An Open-Source MATLAB toolbox for vibrational biospectroscopy
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Dataset representing estimation.
These datasets are outputted by a classifier, clssr::use() method
Definition at line 4 of file estimato.m.
Inheritance diagram for estimato: Collaboration diagram for estimato:Public Member Functions | |
| function | estimato (in o) |
| function | change_classlabels (in o, in clnew) |
| function | copy_from_data (in o, in data) |
| Copies relevant properties from dataset. More... | |
| function get | no (in data) |
| no getter More... | |
| function get | nf (in data) |
| nf getter More... | |
| function get | nonf (in data) |
| nonf getter More... | |
| function get | no_groups (in data) |
| no_groups getter More... | |
| function get | nc (in data) |
| nc getter More... | |
| function get | width (in data) |
| function | get_groupidxs_from_groupcodes (in data, in codes) |
| function | get_obsidxs_from_groupidxs (in data, in groupidxs) |
| function | get_no_levels (in data) |
| Counts to pre-allocate. More... | |
| function | check (in data) |
| Checks if internal variables are synchronized with some troubleshooting. More... | |
| function | import_from_struct (in data, in DATA) |
| function | eliminate_unused_classlabels (in data) |
| function | mount_from_signal (in signal, in no_inputs, in future) |
| Populates from a time series. More... | |
| function | get_props_to_copy (in data) |
| This is the maximum number of rows of the dataset before something blows. More... | |
| function | copy_emptyrows (in data) |
| function | split_map (in data, in map, in feamap, in fext) |
| function | split_splitidxs (in data) |
| prepares a clone, except for the fields in rowfieldnames More... | |
| function | map_rows (in data, in idxnew) |
| function | select_features (in data, in idxs) |
| function | transform_linear (in data, in L, in L_fea_prefix) |
| irverbose(sprintf('INFO (data_select_features()): # features before: %>d; # features after: %>d. ', nfold, data.nf)); More... | |
| function | get_fea_names (in data, in idxs) |
| Returns the names of the features. More... | |
| function | make_groupnumbers (in data) |
| fills in the groupnumbers property based on the groupcodes property. More... | |
| function | assert_fix (in data) |
| Makes the dataset properties consistent with each other. More... | |
| function | get_weights (in data, in exponent) |
| function | transpose2 (in data) |
| function | assert_not_nan (in data) |
| Asserts that there is no NaN in data.X. More... | |
| function | get_description (in o, in flag_short) |
| function | setbatch (in o, in params) |
| Sets several properties of an object at once. More... | |
| function | get_methodname (in o, in flag_short) |
| function | get_report (in o) |
| Object reports are plain text. HTML would be cool but c'mon, we don't need that sophistication. More... | |
| function | get_html (in o, in flag_stylesheet) |
| function | get_params (in o, in data) |
| Calls Parameters GUI. More... | |
| function | extract_log (in o) |
| function | get_ancestry (in o, in flag_title) |
Public Attributes | |
| Property | no |
| number of "observations" (e.g. spectra) More... | |
| Property | nf |
| number of features (i.e., variables) More... | |
| Property | nonf |
| a vector [no, nf] More... | |
| Property | no_groups |
| number of groups More... | |
| Property | nc |
| number of classes More... | |
| Property | X |
| [no]x[nf] matrix. Data matrix More... | |
| Property | classes |
| Property | classlabels |
| Cell of strings. Class labels. More... | |
| Property | groupcodes |
| (optional) [no]x[1] Cell of strings. Group codes (e.g. patient names) More... | |
| Property | obsnames |
| (optional) [no]x[1] Cell of strings. Observation names (e.g. file names of the individual spectra) More... | |
| Property | filename |
| Property | filetype |
| mat or txt More... | |
| Property | fea_x |
| feature x-axis More... | |
| Property | fea_names |
| (optional) Cell of strings. Name of each feature More... | |
| Property | xname |
| x-axis name, defaults to 'Wavenumber (cm^{-1})' More... | |
| Property | xunit |
| x-axis unit, defaults to 'cm^{-1}' More... | |
| Property | yname |
| y-axis name, defaults to 'Absorbance' More... | |
| Property | yunit |
| y-axis unit, defaults to 'a.u.' More... | |
| Property | height |
| Height of image. Spectra start counting from the bottom left upwards. More... | |
| Property | width |
Width of image. Width is actually calculated as no/height . If result is not integer, an error will occur. More... | |
| Property | direction |
| Property | Y |
| Output (instead of classes). For regression instead of classification. More... | |
| Property | groupnumbers |
| For easier access than groupcodes. More... | |
| Property | obsids |
| Property | splitidxs |
| Property | title |
| Property | color |
Protected Member Functions | |
| function | do_get_html (in o) |
| HTML inner body. More... | |
| function | do_get_report (in o) |
| Default report. More... | |
Protected Attributes | |
| Property | rowfieldnames |
| fields to be split or merged when dataset is split or merged More... | |
| Property | flags_cell |
| Property | classtitle |
| Class Title. Should have a descriptive name, as short as possible. More... | |
| Property | short |
| Short for the method name. More... | |
| Property | flag_params |
| Property | flag_ui |
| (GUI setting) Whether to "publish" in blockmenu and datatool. Note that a class can be "published" without a GUI (set flag_params=0 in this case, at the class constructor). More... | |
| Property | moreactions |
| (GUI setting) String cell containing names of methods that may be called from the GUIs More... | |
| function estimato::estimato | ( | in | o | ) |
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Makes the dataset properties consistent with each other.
This is both an assertion routine and a "fixing" routine. The two parts are implemented sequentially, so it will be easy to split this in the future.
The assertion part will do a number of checks and throw an error if there is no hope of making it a consistent dataset. Fatal problems will be:
The subsewquent fix part may do a number of works on the dataset:
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Asserts that there is no NaN in data.X.
| function estimato::change_classlabels | ( | in | o, |
| in | clnew | ||
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This function expects X to represent supports for each class. With the new class labels, it will expand and reorganize X, with the supports the previously non-existing classes being 0, obviously.
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Checks if internal variables are synchronized with some troubleshooting.
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Makes copy with empty fields whose names are in .rowfieldnames Additionally, resets .height
| function estimato::copy_from_data | ( | in | o, |
| in | data | ||
| ) |
Copies relevant properties from dataset.
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HTML inner body.
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Default report.
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retains only labels corresponding to classes that exist in the dataset, and classes are renumbered accordingly
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| o |
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| flag_title=1 |
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Returns description string
Precedence according with flag_short:
| flag_short=0 | I am sealing this to make sure that no class will try to improvise on this function. |
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Returns the names of the features.
This function checks the fea_names property and if it is empty, it makes feature names on-the-fly using the fea_x property.
| idxs | Optional list of indexes to be returned |
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Converts group codes to group indexes Indexes will point to the "unique(data.groupcodes)" vector
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| flag_stylesheet=1 | Whether to include the stylesheet in the HTML |
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This is used only to compose sequence string e.g. xxx->yyy->zzz
| flag_short=0 |
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Counts to pre-allocate.
Loops again to fill Returns the number of levels in classlabels
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Converts group indexes to observation indexes CAUTION: be sure that idxs_codes contains indexes that point to the "unique(data.groupcodes)" vector
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Calls Parameters GUI.
If flag_params, tries uip_<class>.m. If fails, tries uip_<ancestor>.m and so on
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This is the maximum number of rows of the dataset before something blows.
Mounts X and Y each data row will stand for [s(n) s(n-1) s(n-2) ...]. This way the dot product between the row and the coefficients of a linear filter is a causal convolution. Gets a list with all properties except the ones that will be split
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Object reports are plain text. HTML would be cool but c'mon, we don't need that sophistication.
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Gets weights for each class
Weights are inversely proportional to the number of observations in each class.
Weights are normalized, so that their sum equals one
| exponent | =1. Exponent to power all weights before they are normalized to sum=1 |
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Copies structure fields to object fields Contains a dictionary with many old property names for backward compatibility Also works when the input is an object.
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fills in the groupnumbers property based on the groupcodes property.
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Maps rows. Single-output version of split_map()
Returns new object
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Populates from a time series.
This function makes X and Y. X will be a Toeplitz matrix.
Inputs:
| signal | vector s(n) |
| no_inputs | dimensionality of the input data space (aka number of features or nf) |
| future | "prediction task", which will be to predict s(n+future) |
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nc getter
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nf getter
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no getter
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no_groups getter
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nonf getter
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Manual feature selection.
Inputs: idxs: list of column indexes to select, or cell thereof
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Sets several properties of an object at once.
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| params | Cell followint the pattern{'property1', value1, 'property2', value2, ...} |
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Splits dataset into one or more datasets using row maps
| map | 1D or 2D cell array of row indexes |
| feamap | (optional |
| out | Matrix of datasets. |
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prepares a clone, except for the fields in rowfieldnames
maps the rowfieldnames fields be used or not as necessary and no error will occur. Splits dataset into one or more datasets using its own splitidxs property
| map | 1D or 2D cell array of row indexes |
| out | Matrix of datasets. |
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irverbose(sprintf('INFO (data_select_features()): # features before: %>d; # features after: %>d.
', nfold, data.nf));
Transforms dataset using loadings matrix L
data.X = data.X*L; data.xlabel = 'Factor'; data.ylabel = 'Score';
| L[nf][any] | Loadings matrix |
| L_fea_prefix=[] | Prefix to make new feature names. |
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Changes direction and swaps width and height
This is called "transpose2" because MATLAB objects have a built-in "transpose" already
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[no]x[1] vector. Classes. Zero-based (first class is class zero).
Classes may be negative, with special meanings for negative values (see get_negative_meaning.m)
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=1. (GUI setting) Whether to call a GUI when the block is selected in blockmenu.m . If true, a routine called "uip_"<class name> will be called.
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1.8.9.1 
