Add code snippets

matlab/catalog/CatalogFilterNaN.m

@@ -0,0 +1,40 @@
+% function [Catalog] = CatalogFilterNaN(fullcatalog,...)
+% Select lines/values from catalog without NaN and empty string
+% Input parameters are pairs:
+%   names of fields
+%   eg. CatalogSelectRange(fullcatalog,'Mw','EID')
+%
+% (c) Dorota Olszewska IG PAS
+
+function [Catalog] = CatalogFilterNaN(fullcatalog,varargin)
+    Catalog = fullcatalog ;
+    range = true(size(fullcatalog(1).val)) ;
+    na_varargin = numel(varargin) ;
+    for i= 1:na_varargin
+        if ~ischar(varargin{i})
+            warning(['Wrong type of parameter ' num2str(i)])
+            continue
+        end
+        index = find(strcmp(varargin{i},{fullcatalog.field})) ;
+        if length(index) ~= 1
+            warning(['Can not select field ' varargin{i}])
+            continue
+        end
+        if fullcatalog(index).type == 3
+            for ii=1:length(Catalog(index).val)
+            lrange(ii,1) = ~isempty(Catalog(index).val{ii});
+            end
+         else
+            lrange = ~isnan(fullcatalog(index).val) ;
+        %nnel = numel(lrange) ;
+        end
+        range = range & lrange;
+    end
+    for i = 1:numel(fullcatalog)
+        if fullcatalog(i).type == 3
+            Catalog(i).val =  {fullcatalog(i).val{range}}' ;
+        else
+            Catalog(i).val =  fullcatalog(i).val(range) ;
+        end
+    end
+end

matlab/catalog/CatalogSelectFields.m

@@ -0,0 +1,55 @@
+% function [Catalog] = CatalogSelectFields(fullcatalog,...)
+% Select fields from IS-POIG catalog v2.0
+% Produce reduced IS-POIG catalog v2.0
+% Input parameters are names of fields
+%  eg. CatalogSelectFields(fullcatalog,'Date','Lat','Long','Mw')
+%  or cells with names of fields  
+%  eg. CatalogSelectFields(fullcatalog,{'Date','Lat','Long','Mw'})
+%
+% (c) Jan Wiszniowski IG PAS
+% v_2.0 19-09-2016 Dorota Olszewska 
+% 2021-10-22: test of inputs and error messages.
+%
+function [Catalog] = CatalogSelectFields(fullcatalog,varargin)
+    na_varargin = length(varargin) ;
+    no_cols = 0 ; 
+    for i= 1:na_varargin
+        if iscell(varargin{i})
+            cellin = varargin{i} ;
+            for j= 1:numel(cellin)
+                if ischar(cellin{j})
+                    if ~any(strcmp(cellin{j},{fullcatalog.field}))
+                        error('Field %s does not exist in the catalog', cellin{j})
+                    end
+                    no_cols = no_cols+1 ;
+                else
+                    error('Wrong %d{%d} input argument of the CatalogSelectFields function', j, i)
+                end
+            end
+        elseif ischar(varargin{i})
+            if ~any(strcmp(varargin{i},{fullcatalog.field}))
+                error('Field %s does not exist in the catalog', varargin{i})
+            end
+            no_cols = no_cols+1 ;
+        else
+            error('Wrong %d input of the CatalogSelectFields function', i)
+        end
+    end
+    Catalog = struct('field',cell(1,no_cols),'type',cell(1,no_cols),'val',cell(1,no_cols),'unit',cell(1,no_cols),'description',cell(1,no_cols),'fieldType',cell(1,no_cols)) ;
+    no_cols = 0 ; 
+    for i= 1:na_varargin
+        if iscell(varargin{i})
+            cellin = varargin{i} ;
+            for j= 1:numel(cellin)
+                if ischar(cellin{j})
+                    no_cols = no_cols+1 ;
+                    Catalog(no_cols) = fullcatalog(strcmp(cellin{j},{fullcatalog.field})) ;
+                end
+            end
+        elseif ischar(varargin{i})
+            no_cols = no_cols+1 ;
+            Catalog(no_cols) = fullcatalog(strcmp(varargin{i},{fullcatalog.field})) ;
+        end
+    end
+end
+

matlab/catalog/CatalogSelectRange.m

@@ -0,0 +1,83 @@
+% function [Catalog] = CatalogSelectRange(fullcatalog,...)
+% Select lines/values from catalog
+% Input parameters are pairs:
+%   names of fields
+%   and
+%   range of values
+%   for numeric there are: [minval maxval] or [val] or {val1, val2, val3, ...}
+%   for strings there are: 'valtext' or {'valtext1', 'valtext2', 'valtext3', ...}
+%   eg. CatalogSelectRange(fullcatalog,'Mw',[0 4.5])
+%
+% (c) Jan Wiszniowski IG PAS
+%     Modyfied 2016.02.04 - numerical comparison with tolerance 1e-14 
+
+function [Catalog] = CatalogSelectRange(fullcatalog,varargin)
+    Catalog = fullcatalog ;
+    range = true(size(fullcatalog(1).val)) ;
+    na_varargin = numel(varargin) ;
+    for i= 1:2:na_varargin-1
+        if ~ischar(varargin{i})
+            warning(['Wrong type of parameter ' num2str(i)])
+            continue
+        end
+        index = find(strcmp(varargin{i},{fullcatalog.field})) ;
+        if length(index) ~= 1
+            warning(['Can not select field ' varargin{i}])
+            continue
+        end
+        if fullcatalog(index).type == 3
+            lrange = varargin{i+1} ;
+            if ischar(lrange)
+                range = range & strcmp(lrange,fullcatalog(index).val) ;
+            elseif iscell(lrange)
+                l_range = false(size(range)) ;
+                for j = 1:numel(lrange)
+                    llrange = lrange{j} ;
+                    if ischar(llrange)
+                        l_range = l_range | strcmp(llrange,fullcatalog(index).val) ;
+                    end
+                end
+                range = range & l_range ;
+            else
+                warning(['Wrong type of walues for parameter ' varargin{i}])
+            end    
+        else
+            lrange = varargin{i+1} ;
+            nnel = numel(lrange) ;
+            if isnumeric(lrange)
+                tol = abs(lrange) ./ 1e15 ; 
+                if nnel == 2
+                    range = range & fullcatalog(index).val >= lrange(1)-tol(1) &  fullcatalog(index).val <= lrange(2)+tol(2) ;
+                elseif nnel == 1
+                    range = range & abs(fullcatalog(index).val - lrange(1)) <= tol(1) ;
+                end                
+            elseif iscell(lrange)
+                l_range = false(size(range)) ;
+                for j = 1:numel(lrange)
+                    llrange = lrange{j} ;
+                    tol = abs(llrange) ./ 1e15 ; 
+                    if isnumeric(llrange)
+                        if  numel(llrange) == 2
+                            l_range = l_range | fullcatalog(index).val >= llrange(1)-tol(1) &  fullcatalog(index).val <= llrange(2)+tol(2) ;
+                        elseif numel(llrange) == 1
+                            l_range = l_range | abs(range & fullcatalog(index).val - llrange(1)) <= tol(1); 
+                        end
+                    else
+                        warning(['Wrong type of walues for parameter ' varargin{i}])
+                    end
+                end
+                range = range & l_range ;
+            else
+                warning(['Wrong type of walues for parameter ' varargin{i}])
+            end    
+        end
+    end
+    for i = 1:numel(fullcatalog)
+        if fullcatalog(i).type == 3
+            Catalog(i).val =  {fullcatalog(i).val{range}}' ;
+        else
+            Catalog(i).val =  fullcatalog(i).val(range) ;
+        end
+    end
+end
+

matlab/catalog/eliminateEmptyValues.m

@@ -0,0 +1,24 @@
+%
+% -----------------
+% Copyright © 2019 ACK Cyfronet AGH, Poland. 
+%
+% This work was partially funded by EPOS Project funded in frame of PL-POIR4.2
+% --------------
+%
+function varargout = eliminateEmptyValues(varargin)
+    if isempty(varargin)
+        return;
+    end
+    indexes = 1:length(varargin{1});
+    for i = 1:length(varargin)
+        column = varargin{i};
+        if isnumeric(column)
+            indexes = intersect(indexes, find(~isnan(column)));
+        elseif iscell(column)
+            indexes = intersect(indexes, find(~cellfun(@isempty, column)));
+        end
+    end
+    for i = 1:length(varargin)
+        varargout{i} = varargin{i}(indexes);
+    end
+end

matlab/catalog/extractColumns.m

@@ -0,0 +1,25 @@
+%
+% -----------------
+% Copyright © 2019 ACK Cyfronet AGH, Poland. 
+%
+% This work was partially funded by EPOS Project funded in frame of PL-POIR4.2
+% --------------
+%
+function [varargout] = extractColumns(catalog, varargin)
+    for i=1:length(varargin)
+        colName = varargin{i};
+        varargout{i} = findColumn(catalog, colName);
+    end
+end
+
+function column = findColumn(catalog, colName)
+    for c=1:length(catalog)
+        if strcmp(catalog(c).field, colName)
+            column = catalog(c).val;
+            break;
+        end
+    end
+    if exist('column') ~= 1
+        error('no column named %s', colName);
+    end
+end

matlab/catalog/findCatalogColumn.m

@@ -0,0 +1,19 @@
+%
+% -----------------
+% Copyright © 2022 ACK Cyfronet AGH, Poland.
+% --------------
+%
+% Returns index of the column with the specified colName within the given catalog
+%
+% TODO use this function in extractColumns.m
+function columnIdx = findCatalogColumn(catalog, colName)
+    for c=1:length(catalog)
+        if strcmp(catalog(c).field, colName)
+            columnIdx = c;
+            break;
+        end
+    end
+    if exist('columnIdx') ~= 1
+        error('no column named %s', colName);
+    end
+end

matlab/catalog/merge2Catalog.m

@@ -0,0 +1,100 @@
+% function [Catalog] = merge2Catalog(catalog1,catalog2)
+% Add values from 1st Catalog to 2nd
+% 
+% v1.1 - 2021119 - sort according by time was added
+% (c) Dorota Olszewska IG PAS
+
+function [Catalog] = merge2Catalog(Catalog,catalog2,ID)
+
+if sum(strcmp(ID,{Catalog.field}))+sum(strcmp(ID,{catalog2.field})) == 0
+    error([ID,' is not field of both catalogs ', ID])
+end
+
+ID1=Catalog(strcmp(ID,{Catalog.field})).val;
+ID2=catalog2(strcmp(ID,{catalog2.field})).val;
+
+if length(unique(ID1))~=length(ID1) || length(unique(ID2))~=length(ID2)
+    error([ID,' has not unique variable at both catalogs '])
+end
+
+no_cols = size(Catalog,2);
+
+for j = 1:numel(ID2)
+    llrange = ID2{j} ;
+    l_range(j) = sum(strcmp(llrange,ID1)) ;
+end
+
+catalog2_row=CatalogSelectRange(catalog2,ID,catalog2(strcmp(ID,{catalog2.field})).val(l_range==0));
+
+
+% add rows by RID
+no_rows_row = size(catalog2_row(1).val,1);
+if no_rows_row == 0
+else
+for i=1:no_cols
+    if Catalog(i).type == 3
+        if sum(strcmp(Catalog(i).field,{catalog2_row.field})) == 0
+        Catalog(i).val=[Catalog(1).val;repmat({'NaN'},no_rows_row,1)];
+        else
+        Catalog(i).val=[Catalog(i).val;catalog2_row(strcmp(Catalog(i).field,{catalog2_row.field})).val];
+        end
+    else
+        if sum(strcmp(Catalog(i).field,{catalog2_row.field})) == 0
+        Catalog(i).val=[Catalog(i).val;NaN(no_rows_row,1)];
+        else
+        Catalog(i).val=[Catalog(i).val;catalog2_row(strcmp(Catalog(i).field,{catalog2_row.field})).val];
+        end
+    end  
+  
+end
+end
+
+ID1=Catalog(strcmp(ID,{Catalog.field})).val;
+ID2=catalog2(strcmp(ID,{catalog2.field})).val;
+
+no_cols = size(Catalog,2);
+no_rows = size(Catalog(1).val,1);
+
+for j = 1:numel(ID2)
+    llrange = ID2{j} ;
+    l_range(j) = sum(strcmp(llrange,ID1)) ;
+end
+
+catalog2_col=CatalogSelectRange(catalog2,ID,catalog2(strcmp(ID,{catalog2.field})).val(l_range==1));
+
+
+% add columns by RID
+no_rows_col = size(catalog2_col(1).val,1);
+if no_rows_col == 0
+else
+   
+column1={Catalog.field};
+column2={catalog2_col.field};
+  
+
+for j = 1:numel(column2)
+    llrange2 = column2{j} ;
+    l_range2(j) = sum(strcmp(llrange2,column1)) ;
+end
+
+new_column=column2(l_range2==0);
+
+for k=1:numel(new_column)
+    Catalog(no_cols+k).field = catalog2_col(strcmp(new_column{k},{catalog2_col.field})).field;
+    Catalog(no_cols+k).type = catalog2_col(strcmp(new_column{k},{catalog2_col.field})).type;
+    Catalog(no_cols+k).unit = catalog2_col(strcmp(new_column{k},{catalog2_col.field})).unit;
+    Catalog(no_cols+k).description = catalog2_col(strcmp(new_column{k},{catalog2_col.field})).description;
+    Catalog(no_cols+k).fieldType = catalog2_col(strcmp(new_column{k},{catalog2_col.field})).fieldType;
+    for kk=1:no_rows
+        rr=strcmp(Catalog(strcmp(ID,{Catalog.field})).val(kk),catalog2_col(strcmp(ID,{catalog2_col.field})).val);
+        if sum(rr) ==0
+            Catalog(no_cols+k).val(kk,1)=NaN;
+        else
+            Catalog(no_cols+k).val(kk,1) = catalog2_col(strcmp(new_column{k},{catalog2_col.field})).val(rr);
+        end
+    end
+end
+
+Catalog = sortByTime(Catalog);
+
+end

matlab/catalog/modifyCatalog.m

@@ -0,0 +1,90 @@
+ %
+ % -----------------
+ % Copyright © 2022 ACK Cyfronet AGH, Poland.
+ %
+ % Licensed under the Apache License, Version 2.0 (the "License");
+ % you may not use this file except in compliance with the License.
+ % You may obtain a copy of the License at
+ %
+ % http://www.apache.org/licenses/LICENSE-2.0
+ %
+ % Unless required by applicable law or agreed to in writing, software
+ % distributed under the License is distributed on an "AS IS" BASIS,
+ % WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ % See the License for the specific language governing permissions and
+ % limitations under the License.
+ %
+ % This work was partially funded by EPOS-SP Project.
+ % -----------------
+ %
+ % Modifies event with the given 'eventId' in the catalog. If such event was not yet present in the catalog,
+ % it is added at the correct position with respect to time (the event is added at the end and the resulting
+ % catalog is sorted by time)
+ %
+function outCatalog = modifyCatalog(catalog, eventId, eventValues)
+  newColIdxs = findAbsentFields({eventValues.field}, {catalog.field});
+  if ~isempty(newColIdxs)
+    % add columns that were not yet present in the catalog, but are specified in eventValues
+    outCatalog = insertColumns(catalog, eventValues, newColIdxs);
+  else
+    outCatalog = catalog;
+  end
+  idColumn = outCatalog(1).val; % assuming ID is always the first column
+  eventIdx = find(strcmp(idColumn, eventId));
+  isNewEvent = 0;
+  if isempty(eventIdx)
+    isNewEvent = 1;
+    eventIdx = length(idColumn) + 1;
+    outCatalog(1).val(eventIdx) = eventId;
+  end
+  for e=1:length(eventValues)
+    colIdx = findCatalogColumn(outCatalog, eventValues(e).field);
+    outCatalog(colIdx).val(eventIdx) = eventValues(e).value;
+  end
+  if isNewEvent
+    % fill fields that were not specified in eventValues with empty values
+    absentColIdxs = findAbsentFields({outCatalog.field}, {eventValues.field});
+    if ~isempty(absentColIdxs)
+      for i=2:length(absentColIdxs) % skip 1 (ID column index)
+        absColIdx = absentColIdxs(i);
+        outCatalog(absColIdx).val(eventIdx) = getEmptyFieldValue(outCatalog(absColIdx).type, 1);
+      end
+    end
+  end
+  outCatalog = sortByTime(outCatalog);
+end
+
+% find Catalog columns that were not used in eventValues
+function colIdxs = findAbsentFields(catalogFields, eventValuesFields)
+  colIdxs = [];
+  for c=1:length(catalogFields)
+    if ~ismember(catalogFields(c), eventValuesFields)
+      colIdxs(end + 1) = c;
+    end
+  end
+end
+
+% get value that should be used as empty field for the given column type
+function empty = getEmptyFieldValue(type, fieldsNo)
+   if (type == 3)
+     empty = cell(fieldsNo, 1);
+   else
+     empty = nan(fieldsNo, 1);
+   end
+end
+
+function outCatalog = insertColumns(catalog, eventValues, newColIdxs)
+  outCatalog = catalog;
+  rowsNo = length(catalog(1).val);
+  colsNo = length(catalog);
+  for i=1:length(newColIdxs)
+    newColIdx = colsNo+i;
+    eventFields = eventValues(newColIdxs(i));
+    outCatalog(newColIdx).field = eventFields.field;
+    outCatalog(newColIdx).type = eventFields.type;
+    outCatalog(newColIdx).unit = eventFields.unit;
+    outCatalog(newColIdx).description = eventFields.description;
+    outCatalog(newColIdx).fieldType = eventFields.fieldType;
+    outCatalog(newColIdx).val = getEmptyFieldValue(eventFields.type, rowsNo);
+  end
+end

matlab/catalog/sortByTime.m

@@ -0,0 +1,10 @@
+function [sortedCatalog] = sortByTime(catalog)
+  timeColIndex = find(strcmp('Time', {catalog.field}));
+  if ~isempty(timeColIndex)
+      [~, sortedIndexes] = sortrows(catalog(timeColIndex).val);
+      for i=1:length(catalog)
+          catalog(i).val = catalog(i).val(sortedIndexes);
+      end
+  end
+  sortedCatalog = catalog;
+end

matlab/catalog/test

@@ -0,0 +1 @@
+filterByMminAndTime