ISIS 3 Application Documentation
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Perform NoiseFilter processing in the Pipeline Enviornment.
Description
Categories
Groups
History
Description
This application removes noise from HiRISE cubes. It also checks the pause points and removes any artifacts there. The application runs in a pipeline and starts off by getting the histogram of the image and gets the standard deviation, percentage of LIS pixels and MaxDN from the histogram stats. It then runs Cubenorm and processes the cubenorm stats given the Channel and Summing mode. If percentage of valid pixels in a column is less than CLEAR_FRACTION and if NULL_COLUMNS option is set then the stats for the columns Average, Median, StdDev, Minimum, Maximum will be set to 0 else it is set to 1. These changes are ouputted to new Stats files.
For images with summing equal to 1, depending on Channel 0/1, pause, width and direction is calculated. If the percentage of valid pixels in these columns are less than the user specified NONVALID_FRACTION then these columns are said to contain a high percentage of non-valid pixels and the stats for the columns stated above are set to 0.
These updated stats will form the input stats for cubenorm app which is run twice and output of which forms the input image one each for lowpass and highpass filters. The cubenorm basically clears the columns with stats equal to 0 which was previously manipulated. Perform highpass and lowpass filters for vertical destripping. The lowpass app is run with the options LPF_LINES, LPF_SAMPLES, LPF_MINPER. The highpass app is run with the options HPF_LINES, HPF_SAMPLES, HPF_MINPER. The output of these 2 filters are added.
Noisefilter app is run 3times with the options FLATTOL, TOLDEF, TOLMIN, TOLMAX, LOW, HIGH, REPLACE, SAMPLE, LINE, LISISNOISE and LRSISNOISE.
Now that the data is much cleaner another set of lowpass, highpass filters are performed on the image and added togather. This is the final product for non RED image.
Perform LPFZ filters if we have a RED filter image. For IR and BG filter data, assume that the HiColorNorm pipeline step will interpolate using the BG/RED and IR/RED ratio data. So another set of lowpass and highpass filters is performed on RED filter image and added to get the final product.
Categories
Parameter Groups
Files
| Name | Description |
|---|---|
| FROM | Input file |
| TO | Output file |
| REMOVE | Remove Intermediate Files |
Low Pass Filter Options
| Name | Description |
|---|---|
| LPF_LINES | lowpass LINES parameter for the boxcar |
| LPF_SAMPLES | lowpass SAMPLES parameter for the boxcar |
| LPF_MINPER | lowpass MINIMUM parameter (as a percentage) |
High Pass Filter Options
| Name | Description |
|---|---|
| HPF_LINES | highpass LINES parameter for the boxcar |
| HPF_SAMPLES | highpass SAMPLES parameter for the boxcar |
| HPF_MINPER | highpass MINIMUM parameter (as a percentage) |
Noise Filter Options
| Name | Description |
|---|---|
| NULL_COLUMNS | Flag to NULL columns |
| TOLMIN | Dark noise tolerance |
| TOLMAX | Bright noise tolerance |
| FLATTOL | Scaled tolerance value |
| MIN_VALUE | Valid minimum pixel |
| HARD_TOLMIN | noisefilter TOLMIN parameter for hard noise filtering |
| HARD_TOLMAX | noisefilter TOLMAX parameter for hard noise filtering |
| LPFZ_LINES | lowpass LINES parameter for LPFZ |
| LPFZ_SAMPLES | lowpass SAMPLES parameter for LPFZ |
| NOISE_SAMPLES | Number of samples in boxcar |
| NOISE_LINES | Number of lines in boxcar |
| CLEAR_FRACTION | NULL any columns with valid pixel less than this value |
| NONVALID_FRACTION | Pause point tolerance fraction |
| HARD_FILTERING | Percent of LIS pixels to switch to hard noise filtering |
| HIGHEND_PERCENT | Fraction of high-end pixels to zap |
| HARD_HIGHEND_PERCENT | Fraction of high-end pixels to zap for hard noise filtering |
Files: FROM
Description
Input cube to remove noise from
| Type | cube |
|---|---|
| File Mode | input |
| Filter | *.cub |
Files: TO
Description
Output cube with noise removed
| Type | cube |
|---|---|
| File Mode | output |
| Pixel Type | real |
Files: REMOVE
Description
Remove Intermediate Files
| Type | boolean |
|---|---|
| Default | false |
Low Pass Filter Options: LPF_LINES
Description
This is the total number of lines in the boxcar. It must be odd and can not exceed twice the number of lines in the cube.
| Type | integer |
|---|---|
| Default | 251 |
Low Pass Filter Options: LPF_SAMPLES
Description
This is the total number of samples in the boxcar. It must be odd and can not exceed twice the number of samples in the cube.
| Type | integer |
|---|---|
| Default | 3 |
Low Pass Filter Options: LPF_MINPER
Description
Minimum boxcar pixels required for filter. This option is the minimum number of valid pixels required in a boxcar for filtering to begin.
| Type | integer |
|---|---|
| Default | 5 |
High Pass Filter Options: HPF_LINES
Description
This is the total number of lines in the boxcar. It must be odd and can not exceed twice the number of lines in the cube.
| Type | integer |
|---|---|
| Default | 251 |
High Pass Filter Options: HPF_SAMPLES
Description
This is the total number of samples in the boxcar. It must be odd and can not exceed twice the number of samples in the cube.
| Type | integer |
|---|---|
| Default | 1 |
High Pass Filter Options: HPF_MINPER
Description
Minimum boxcar pixels required for filter. This option is the minimum number of valid pixels required in a boxcar for filtering to begin.
| Type | integer |
|---|---|
| Default | 5 |
Noise Filter Options: NULL_COLUMNS
Description
This option indicates whether columns with valid pixels with ratio with Max Valid pixels less than CLEAR_FRACTION must be NULLed.
| Type | boolean |
|---|---|
| Default | FALSE |
Noise Filter Options: TOLMIN
Description
If the difference between the input pixel and the boxcar average is greater then the tolerances given in TOLMIN or TOLMAX (values of DN), the pixel is considered to be noise and will be replaced. When a pixel is being checked for noise, a difference between the pixel and boxcar average is computed. If this difference is negative then TOLMIN will be used to determine if we have noise, hence dark noise will be removed by modifying TOLMIN.
| Type | double |
|---|---|
| Default | 3.5 |
Noise Filter Options: TOLMAX
Description
If you are attempting to remove white speckle or other bright noise then you should be modifying this parameter. When a pixel is being checked for noise, a difference between the pixel and boxcar average is computed. If this difference is positive then TOLMAX will be used to determine if we have noise, hence white noise will be removed by modifying TOLMAX.
| Type | double |
|---|---|
| Default | 3.5 |
Noise Filter Options: FLATTOL
Description
Minimum tolerance value used in the STDDEV filter. If the difference between the original pixel, and the average value of the noise filter is less than the FLATTOL then the output pixel will remain unchanged from the input pixel. Without this safeguard, very uniform inage areas (low standard deviation) will be excessively smoothed, creating areas of constant DN.
| Type | double |
|---|---|
| Default | 1 |
Noise Filter Options: MIN_VALUE
Description
Valid minimum pixel value that will be used in boxcar computation. If a pixel value is less than LOW then it will not be used when computing boxcar statistics.
| Type | double |
|---|---|
| Default | 0 |
Noise Filter Options: HARD_TOLMIN
Description
Use this value for noisefilter's TOLMIN parameter when doing hard noise filtering
| Type | double |
|---|---|
| Default | 3.5 |
Noise Filter Options: HARD_TOLMAX
Description
Use this value for noisefilter's TOLMAX parameter when doing hard noise filtering
| Type | double |
|---|---|
| Default | 3.5 |
Noise Filter Options: LPFZ_LINES
Description
| Type | integer |
|---|---|
| Default | 5 |
Noise Filter Options: LPFZ_SAMPLES
Description
| Type | integer |
|---|---|
| Default | 5 |
Noise Filter Options: NOISE_SAMPLES
Description
This is the total number of samples in the boxcar. It must be odd and can not exceed twice the number of samples in the cube. In general, the size of the boxcar does not cause the program to operate significantly slower. The shape of the filter can be used to control types of noise to remove. For example, a 3x3 or 5x5 boxcar can be used to remove speckle or salt and pepper noise. A 1 sample x 5 line boxcar with REPLACE=NULL could be used to remove dropped or noisy lines of data. Then use the lowpass program with a 3x3 boxcar to fill in the NULLed data.
| Type | integer |
|---|---|
| Default | 7 |
Noise Filter Options: NOISE_LINES
Description
This is the total number of lines in the boxcar. It must be odd and can not exceed twice the number of lines in the cube. In general, the size of the boxcar does not cause the program to operate significantly slower. The shape of the filter can be used to control types of noise to remove. For example, a 3x3 or 5x5 boxcar can be used to remove speckle or salt and pepper noise. A 1 sample x 5 line boxcar with REPLACE=NULL could be used to remove dropped or noisy lines of data. Then use the lowpass program with a 3x3 boxcar to fill in the NULLed data.
| Type | integer |
|---|---|
| Default | 7 |
Noise Filter Options: CLEAR_FRACTION
Description
Fraction of valid pixels for which a column will not be NULL i.e any columns with valid points percentage less than this value will be set to NULL
| Type | double |
|---|---|
| Default | 0 |
Noise Filter Options: NONVALID_FRACTION
Description
For each column of the cube a count is calculated of the number of valid pixels in the column. If any columns count divided by the maximum count is less than NONVALIDFRACTION then the pause points are nulled out. If the binning is anything other than one then all columns are checked with only the failing columns getting nulled out.
| Type | double |
|---|---|
| Default | 0.90 |
Noise Filter Options: HARD_FILTERING
Description
Percent of LIS pixels to switch to hard noise filtering
| Type | double |
|---|---|
| Default | 0.1 |
Noise Filter Options: HIGHEND_PERCENT
Description
Fraction of high-end pixels to zap
| Type | double |
|---|---|
| Default | 99.999 |
Noise Filter Options: HARD_HIGHEND_PERCENT
Description
Fraction of high-end pixels to zap for hard noise filtering
| Type | double |
|---|---|
| Default | 99.99 |
History
| Sharmila Prasad | 2011-02-04 | Original version converted from Eric Eliason's hical pipeline version 1.42 |
| Sharmila Prasad | 2011-02-22 | Renamed hinoise2 to hinoise. Previous redundant hinoise app has been removed. |
| Sharmila Prasad | 2011-03-02 | Fix App Test - Enable parallel Test runs making input file name as part of unique temp files for pipeline. |