Spitzer Documentation & Tools

Table of Contents

1      What is IRSCLEAN?.

1.1       Should I Always Run IRSCLEAN On My Data?.

1.2       What is This Document?.

1.3       What’s New In IRSCLEAN

1.4       System requirements.

2      Installing IRSCLEAN

2.1       Downloading.

2.2       Unpacking.

2.3       Setting the IDL Path.

2.3.1    Outside of IDL, Unix-type Computers.

2.3.2    Inside of IDL

2.3.3    All IDL Versions, all Operating Systems.

2.4       Mac OS X: Enabling Mouse Cursor Input

2.4.1    In OS X 10.4 (Tiger) and prior:

2.4.2    In OS X 10.5 (Leopard) and later:

2.4.3    Emulate a three-button mouse.

3      The Sample Files.

4      Masks Used or Created by IRSCLEAN

4.1       RMASK: The Rogue Pixel Mask.

4.2       FMASK: The "Found" Mask.

4.3       UMASK: The User-Defined Mask.

4.4       BMASK: The Pipeline BCD Mask.

4.5       OMASK: The Order Mask.

4.6       UNCLEAN_MASK: The Mask of Unsuccsessfully Cleaned Pixels.

5      How to Run IRSCLEAN

5.1       General Syntax.

5.2       Running the Virtual Machine Version of IRSCLEAN

6      Stage 1: Creating And Editing Masks.

6.1       Reading in Data.

6.2       Scaling Image Display.

6.3       Reading a Preexisting Mask (inRmask_File, /CampaignRmask)

6.4       Creating a Mask Manually from Scratch.

6.5       Letting IRSCLEAN Find a Mask Automatically (getFmask)

6.5.1    getFmask=1: the Hierarchical Iterative Method (/getFmask, AGGRESSIVE,/ABS_VAL, /NEGATIVE_ONLY,ORDERS,/peakUp)

6.5.2    getFmask=2:  Double Unsharp-Mask Flattening Method (getFmask=2, Rogue_Thresh,Noise_Floor, AGGRESSIVE,/ABS_VAL,/NEGATIVE_ONLY)

6.6       Specifying Your Own Subroutine for Automatic Mask Finding (maskFunction=, AGGRESSIVE, /ABS_VAL, /NEGATIVE_ONLY)

6.7       Combining Masks.

6.8       Mask-edit Mode.

6.9       Saving Your Mask (outRmask_File)

6.10     Saving Your Cleaned Data (outClean_File)

6.11     Automatically Saving the Rogue Mask and Cleaned Data (/Autosave)

6.12     Skipping Mask-Edit Mode (/noMaskEdit)

6.13     Quitting After Stage 1 (/noStage2)

6.14     Full Batch Mode (getFmask, /CampaignRMask, inRmask_File, /noMaskEdit, /autoSave, /noStage2)

7      Stage 2: Cleaning A Set of Data.

7.1       Picking Files to Clean (filesToClean)

7.2       Reviewing Files to Clean.

7.3       Cleaning Files.

7.4       "Cleaning" Uncertainty and Mask Files.

8      Using IRSCLEAN Results in SPICE

9      Appendix 1: Hints.

9.1       Automatic Command Line Suggestion.

9.2       Getting Help (/Help)

9.3       Setting the Working Directory (Directory)

9.4       Changing the Default Size of the Displayed Image (WinSize)

9.5       Changing the Default Brightness Scaling of the Displayed Image (dataRange)

9.6       Changing the Default Colors for the Rogue Mask and BMASK (colorNames)

9.7       Adding NaN Pixels to the Rogue Mask (/NAN)

9.8       Using the Cursor Value to Help Find Rogues by Eye.

9.9       A second pass at cleaning data using the unclean_mask file.

10       APPENDIX 2: Limiting Which Orders IRCLEAN_MASK Examines  (/getFmask, ORDERS=)

11    APPENDIX 3: Finding Rogues in and/or Cleaning The Peakup Sub-arrays (/PeakUp)

12    APPENDIX 4: Complete Listing of Command Options.