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Added and tested functionality for 'N/A' stats calculation. (DOI-USGS…
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…#3895)

* Added and tested functionality for 'N/A' stats calculation.

* Added changelog and updated style to conform with isis standards.
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@AustinSanders @jessemapel
AustinSanders authored and jessemapel committed Jun 11, 2020
1 parent 81490a5 commit 1314cfa
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19 changes: 15 additions & 4 deletions isis/src/base/apps/stats/stats.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,17 +21,17 @@ namespace Isis {
* the ISIS3 stats application.
*
* @param ui The User Interface to parse the parameters from
*/
*/
void stats(UserInterface &ui) {
Cube *inputCube = new Cube();

CubeAttributeInput inAtt(ui.GetAsString("FROM"));
inputCube->setVirtualBands(inAtt.bands());

inputCube->open(ui.GetFileName("FROM"));
stats(inputCube, ui);
}

/**
* Compute the stats for an ISIS cube. This is the programmatic interface to
* the ISIS3 stats application.
Expand Down Expand Up @@ -134,6 +134,17 @@ namespace Isis {
results += PvlKeyword("Maximum", toString(stats->Maximum()));
results += PvlKeyword("Sum", toString(stats->Sum()));
}
else {
results += PvlKeyword("Average", "N/A");
results += PvlKeyword("StandardDeviation", "N/A");
results += PvlKeyword("Variance", "N/A");
results += PvlKeyword("Median", "N/A");
results += PvlKeyword("Mode", "N/A");
results += PvlKeyword("Skew", "N/A");
results += PvlKeyword("Minimum", "N/A");
results += PvlKeyword("Maximum", "N/A");
results += PvlKeyword("Sum", "N/A");
}
results += PvlKeyword("TotalPixels", toString(stats->TotalPixels()));
results += PvlKeyword("ValidPixels", toString(stats->ValidPixels()));
results += PvlKeyword("OverValidMaximumPixels", toString(stats->OverRangePixels()));
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83 changes: 43 additions & 40 deletions isis/src/base/apps/stats/stats.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,22 +7,22 @@
<description>
<p>
This program computes a set of statistics for the pixels in each selected <def link="Band">band</def>
of an image <def link="Cube">cube</def>, and outputs the results of each band. By default, all bands are
processed. The <i>stats</i> program generates statistics that will help you find new insights
of an image <def link="Cube">cube</def>, and outputs the results of each band. By default, all bands are
processed. The <i>stats</i> program generates statistics that will help you find new insights
in your data to make more accurate predictions and achieve better outcomes.
</p>


<h4>
Output:
</h4>

<p>
The statistics are output to both the screen and the print.prt file in PVL format. Additionally,
if the user specifies a file using the TO parameter, the statistics are written to that file in
PVL format (default) or as a comma delimited text file (FLAT file), as specified by the FORMAT parameter.
For multi-band images, each band has its own statistics information that will be appended to the
output file. The contents of the PVL file can be read using the <i>getkey</i> program. The
PVL format (default) or as a comma delimited text file (FLAT file), as specified by the FORMAT parameter.
For multi-band images, each band has its own statistics information that will be appended to the
output file. The contents of the PVL file can be read using the <i>getkey</i> program. The
comma delimited text file can be imported into Excel or other applications. The statistics
calculated and reported are as follows:
</p>
Expand All @@ -46,7 +46,7 @@ Maximum Low instrument saturation (LIS) pixels

Sum High instrument saturation (HIS) pixels
</pre>

<p>
If the output file exists and the APPEND parameter is set to "no," the contents will be
overwritten.
Expand All @@ -58,9 +58,9 @@ Sum High instrument saturation (HIS) pixels

<p>
You may process one or a few specific bands if you indicate the band(s) in which you desire
to gather statistics. A <def link="Band">band</def> may be specified by simply placing a
plus sign and the band number after the input filename (e.g., peaks.cub+3). For several
bands, commas and hyphens are used to communicate effectively with the program as in the
to gather statistics. A <def link="Band">band</def> may be specified by simply placing a
plus sign and the band number after the input filename (e.g., peaks.cub+3). For several
bands, commas and hyphens are used to communicate effectively with the program as in the
following example: peaks.cub+2,4-6.
</p>

Expand Down Expand Up @@ -109,21 +109,21 @@ Sum High instrument saturation (HIS) pixels
<change name="Jacob Danton" date="2006-01-23">
Fixed appTest to comply to changes in iString
</change>
<change name="Steven Lambright" date="2008-05-06">
<change name="Steven Lambright" date="2008-05-06">
Added Above Range, Below Range reports
</change>
<change name="Steven Lambright" date="2008-05-13">
Removed references to CubeInfo
Removed references to CubeInfo
</change>
<change name="Steven Lambright" date="2008-08-15">
A bug where the VALIDMIN,VALIDMAX were ignored was fixed;
A bug where the VALIDMIN,VALIDMAX were ignored was fixed;
these should always be used.
</change>
<change name="Stacy Alley" date="2009-01-16">
Added the Format option for the output file.
</change>
<change name="Sharmila Prasad" date="2011-03-31">
Added Band Keyword - displays the first physical band used to get the
Added Band Keyword - displays the first physical band used to get the
stats
</change>
<change name="James Alexander Crough" date="2011-06-17">
Expand All @@ -140,6 +140,9 @@ Sum High instrument saturation (HIS) pixels
general edits for clarity. Also added undocumented output statistics
to the list in the description.
</change>
<change name="Austin Sanders" date="2020-06-04">
Updated to fill columns with N/A in cases where images contained only
special or invalid pixels.
</history>

<oldName>
Expand All @@ -163,8 +166,8 @@ Sum High instrument saturation (HIS) pixels
Input cube
</brief>
<description>
This specifies the input <def link="Cube">cube</def>. The default is
to calculate statistics for each band in the input cube, but this can be
This specifies the input <def link="Cube">cube</def>. The default is
to calculate statistics for each band in the input cube, but this can be
overridden using the band specifier (e.g., file.cub+3).
</description>
<filter>
Expand All @@ -182,8 +185,8 @@ Sum High instrument saturation (HIS) pixels
No output file is created
</internalDefault>
<description>
This text file will contain the statistics for each individual band.
If it is written in PVL format (default), the values can be read using the
This text file will contain the statistics for each individual band.
If it is written in PVL format (default), the values can be read using the
<i>getkey</i> program. This is useful for developing scripts. If it is
written as a comma delimited text file (FLAT) the output can be easily
imported into spreadsheet applications like Excel.
Expand All @@ -199,9 +202,9 @@ Sum High instrument saturation (HIS) pixels
Output file format (PVL or comma delimited text)
</brief>
<description>
This is the format type for the output file. <def>PVL</def> format is the
This is the format type for the output file. <def>PVL</def> format is the
default. The format is ignored unless the TO parameter is specified.
</description>
</description>
<default><item>PVL</item></default>
<list>
<option value="PVL">
Expand All @@ -218,30 +221,30 @@ Sum High instrument saturation (HIS) pixels
Format the output file specified by TO as a comma delimited text file.
</brief>
<description>
Output the results to a comma delimited text file specified by TO.
Output the results to a comma delimited text file specified by TO.
This file format can easily be imported into spreadsheet applications
like Excel.
</description>
</option>
</list>
</parameter>

<parameter name="APPEND">
<type>boolean</type>
<brief>
Append results to output file specified by TO.
</brief>
<description>
<p>
If this option is not selected, the output from the <i>stats</i>
If this option is not selected, the output from the <i>stats</i>
application is appended to the output file. If this option is
set to "NO" or "FALSE," any information in the TO file is
set to "NO" or "FALSE," any information in the TO file is
overwritten.
</p>
<p>
Note: This will append the formatted results to the end of the TO
Note: This will append the formatted results to the end of the TO
file without regard to the formatting of the current contents.
</p>
</p>
</description>
<default><item>TRUE</item></default>
</parameter>
Expand All @@ -258,7 +261,7 @@ Sum High instrument saturation (HIS) pixels
No minimum DN value
</internalDefault>
<description>
The statistics will exclude any <def link="Digital Number">DN</def>
The statistics will exclude any <def link="Digital Number">DN</def>
values below this value.
</description>
</parameter>
Expand All @@ -272,7 +275,7 @@ Sum High instrument saturation (HIS) pixels
No maximum DN value
</internalDefault>
<description>
The statistics will exclude any <def link="Digital Number">DN</def>
The statistics will exclude any <def link="Digital Number">DN</def>
values above this value.
</description>
</parameter>
Expand All @@ -283,17 +286,17 @@ Sum High instrument saturation (HIS) pixels
<example>
<brief>Calculate statistics for all bands in a cube</brief>
<description>
This example shows the statistics computed for all bands in
This example shows the statistics computed for all bands in
the input cube. When no band is specified by the user, <i>stats</i>
default behavior is to calculate statistics for all bands in a cube.
default behavior is to calculate statistics for all bands in a cube.
</description>
<terminalInterface>
<commandLine>
from=peaks.cub to=peaks0_stats.log
</commandLine>
<description>
Command to run stats in the command line mode using all bands in
peaks.cub and output the results to peaks0_stats.log.
Command to run stats in the command line mode using all bands in
peaks.cub and output the results to peaks0_stats.log.
</description>
</terminalInterface>
<dataFiles>
Expand All @@ -309,20 +312,20 @@ Sum High instrument saturation (HIS) pixels
</dataFile>
</dataFiles>
</example>

<example>
<brief>Calculate statistics for a single band from an input cube</brief>
<description>
This example shows the statistics computed from band 3 of the input
cube. A band may be specified by simply placing the plus sign and
This example shows the statistics computed from band 3 of the input
cube. A band may be specified by simply placing the plus sign and
the band number after the input filename.
</description>
<terminalInterface>
<commandLine>
from=peaks.cub+3 to=peaks1_stats.log
</commandLine>
<description>
Command to run stats in the command line mode using the third band
Command to run stats in the command line mode using the third band
of peaks.cub and output the results to peaks1_stats.log.
</description>
</terminalInterface>
Expand All @@ -342,17 +345,17 @@ Sum High instrument saturation (HIS) pixels
<example>
<brief>Calculate statistics for multiple bands from an input cube</brief>
<description>
This example shows the statistics computed for selected bands of a cube.
In addition to the plus suffix, the comma and hyphen are used to specify
multiple bands from the input cube to process.
This example shows the statistics computed for selected bands of a cube.
In addition to the plus suffix, the comma and hyphen are used to specify
multiple bands from the input cube to process.
</description>
<terminalInterface>
<commandLine>
from=peaks.cub+2,4-6 to=peaks2_stats.log
</commandLine>
<description>
Command to run stats in the command line mode using the second, fourth,
fifth, and sixth bands of peaks.cub and output the results to
fifth, and sixth bands of peaks.cub and output the results to
peaks2_stats.log.
</description>
</terminalInterface>
Expand Down
9 changes: 9 additions & 0 deletions isis/tests/statsTests.cpp
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Expand Up @@ -134,6 +134,15 @@ TEST_F(stats_MockHist, TestStats) {
EXPECT_EQ(1, (int) (band2Stats.findKeyword("LrsPixels")));
EXPECT_EQ(1, (int) (band2Stats.findKeyword("HisPixels")));
EXPECT_EQ(1, (int) (band2Stats.findKeyword("HrsPixels")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Average")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("StandardDeviation")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Variance")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Median")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Mode")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Skew")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Minimum")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Maximum")));
EXPECT_TRUE("N/A" == (band2Stats.findKeyword("Sum")));
}

TEST(stats, ValidMinimum) {
Expand Down

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