Optical Array Shadow Imaging Software (OASIS) 1.0

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C O P Y R I G H T © 2 0 1 3 D R O P L E T M E A S U R E M E N T T E C H N O L O G I E S

Optical Array Shadow Imaging Software

(OASIS) 1.0

User Manual

DOC-0350 B-4

2545 Central Avenue Boulder, CO 80301 USA

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2545CENTRAL AVENUE

BOULDER,COLORADO,USA80301 TEL:+1(303)440-5576 FAX:+1(303)440-1965

WWW.DROPLETMEASUREMENT.COM

DMT licenses OASIS software only upon the condition that you accept all of the terms contained in this license agreement. Each OASIS license you purchase allows you to acquire data on one computer only. Data can be viewed in playback mode on an unlimited number of computers.

This software is provided by DMT “as is” and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. Under no circumstances and under no legal theory, whether in tort, contract, or otherwise, shall DMT or its developers be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including damages for work stoppage; computer failure or malfunction; loss of goodwill; loss of use, data or profits; or for any and all other damages and losses).

Some states do not allow the limitation or exclusion of implied warranties and you may be entitled to additional rights in those states.

Trademark Information

All Droplet Measurement Technologies, Inc. product names and the Droplet Measurement Technologies, Inc. logo are trademarks of Droplet Measurement Technologies, Inc.

All other brands and product names are trademarks or registered trademarks of their respective owners.

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1.0 Introduction ... 7

1.1 OASIS Data Format Compatibility ... 7

2.0 Installing OASIS ... 7

2.1 Recommended System Requirements ... 7

2.2 Prerequisites... 8

2.2.1 KeyLok drivers ... 8

2.2.2 IGOR Pro ... 8

2.2.3 PADS Image Data ... 8

2.3 OASIS Package Installer ... 9

2.3.1 Required Files ... 9

2.3.2 Running the Installer ... 9

2.4 Optional Additional Software: HDFView ... 9

3.0 Starting OASIS... 10

4.0 Setting up Input and Output Paths (File I/O Section) ... 11

4.1 Setting the Data Paths ... 11

4.2 Viewing Details of Files in Input and Output Directories ... 13

4.3 Specifying the Probe Type ... 14

4.3.1 Note on File Prefixes ... 16

4.3.2 Troubleshooting Probe Config Issues—Frequently Asked Questions... 16

4.4 Loading PADS .csv data files ... 16

4.4.1 Troubleshooting .csv File Loading ... 17

4.4.2 Viewing Loaded PADS csv Files ... 18

4.5 Other Options Related to File Processing (nProc, GZIP, and Overwrite) ... 19

5.0 Filtering Input Data (Data Queue Section) ... 20

5.1 Filtering Data Files ... 20

5.1.1 Filtering Files by Time Interval ... 20

5.1.2 Filtering Files by File ID or File Name ... 21

5.2 Filtering Particle Types ... 21

5.2.1 Defining Categories for Particle Types ... 21

5.2.2 Selecting a Particle Category to Use as a Filter ... 22

6.0 Setting True Airspeed (TAS Data Section) ... 23

6.1 Why Airspeed Matters ... 23

6.2 Using a Constant TAS ... 23

6.3 Using Measured TAS Data from a File ... 23

6.3.1 Identifying an Appropriate Source for Measured Air Speed Data ... 23

6.3.2 Specifying PADS Channels as Sources for TAS ... 24

6.3.3 Specifying Other Sources for TAS Data ... 25

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6.4 Time Format in IGOR Pro ... 26

7.0 Generating Intermediate HDF Files (Raw Data Processing Section) ... 29

7.1 What the “Process” Button Does ... 29

7.2 Processing Options ... 29

7.3 Starting and Aborting Processing ... 29

8.0 Generating Images (Image Output Section) ... 30

8.1 Requirements ... 30

8.2 Setting Parameters for Image Output ... 31

8.3 Definitions: Slices and Sets ... 31

8.4 What the “Output” Button Does ... 32

9.0 Graphing and Data Analysis (Data Analysis Section) ... 33

9.1 Requirements ... 33

9.2 Overview of Data Analysis Parameters... 33

9.3 One-Dimensional Plots—f(x) Plots ... 34

9.4 Two-Dimensional Plots—f(x,y) Plots... 34

9.5 Setting the Axis Options ... 34

9.5.1 Definitions of Axis Options (Min, Max, Log, and Delta)... 35

9.6 Analysis Options ... 35

9.6.1 Sizing Options ... 35

9.6.2 Options for M-2-D (Mass-Diameter) Relationships ... 36

9.6.3 Sample Area (SA) Options ... 37

9.6.4 Depth of Field Corrections ... 37

9.7 Examples ... 37

9.7.1 Inter-arrival times ... 37

9.7.2 Number Concentration as a Function of Size and Time ... 38

10.0 Exporting Data from OASIS ... 39

Appendix A: Image Processing Description ... 42

References ... 45

Appendix B: Structure of HDF Files... 45

HeaderMatrixWv: Data from Data-Block Buffer Headers ... 46

ParticleTimesWv: Data from Single-Particle Headers ... 47

ParticleStatsWv: Data from Images ... 47

StrNamesWv, StrValuesWv, VarNamesWv, VarValuesWv ... 48

Appendix C: Revisions to Manual ... 48

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Figures

Figure 1: The OASIS GUI Upon Start-Up ... 11

Figure 2: The Set Path Buttons (highlighted in green) ... 12

Figure 3: The Dialog Allowing You to Specify the Data Location ... 12

Figure 4: Selecting the Appropriate Folder ... 12

Figure 5: Accepting the Selected Folder ... 13

Figure 6: OASIS Panel with Input Path Displayed ... 13

Figure 7: Input Data Table ... 14

Figure 8: Edit probe config Button ... 14

Figure 9: OASIS Instrument Table ... 15

Figure 10: Saving Changes to the Probe Config ... 15

Figure 11: Load PADS csv Button... 17

Figure 12: Error Message Displayed When OASIS Encounters an Unexpected Filename ... 17

Figure 13: Opening the IGOR Pro Data Browser ... 18

Figure 14: Locating a PADS Data File within the IGOR Pro Data Browser ... 19

Figure 15: Other File I/O Options ... 20

Figure 16: Data Queue Section of OASIS... 20

Figure 17: OASIS Particle Category Table ... 22

Figure 18: Selecting a Category ... 22

Figure 19: TAS Data Section with a Constant Airspeed of 100 m/sec Selected . 23 Figure 20: Clicking on Arrow to Right of Speed Box ... 24

Figure 21: Selecting PADS File for TAS Source ... 24

Figure 22: Selecting PADS Channel for TAS Source ... 25

Figure 23: Adding Time Correction in IGOR Pro's Command Line ... 26

Figure 24: Root Directory in Data Browser ... 27

Figure 25: Entering the Redimension Command ... 27

Figure 26: Expanding the Digits Displayed in the Data Browser ... 28

Figure 27: Options for Raw File Processing ... 29

Figure 28: Abort Button ... 29

Figure 29: Error Message after Processing has been Aborted ... 30

Figure 30: Image Output Controls... 31

Figure 31: A Particle Slice ... 32

Figure 32: Example Grayscale Images Generated by OASIS ... 32

Figure 33: Data Analysis Parameters ... 33

Figure 34: Max Width, Max Length and Projected Length... 36

Figure 35: Configuration to Generate Simple IAT Analysis Graph ... 38

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Figure 36: Number Concentration as a Function of Particle Inter-arrival Time (IAT). ... 38 Figure 37: Configuration to Generate Simple Number Concentration as a Function

of Time and Size ... 39 Figure 38: Number Concentration as a Function of Time and Particle Size... 39 Figure 39: Export-Data Options in OASIS ... 40 Figure 40: Dialog to Specify File Name and Destination for Exported Data .... 40 Figure 41: A Time Wave in the IGOR Pro Data Browser (left) and the Corresponding

Exported Data in a Tab-Delimited Text File (right). ... 41

Figure 42: Particle Size Derivations Generated by OASIS ... 42

Figure 43: Viewing Generated Waves after Raw File Processing ... 46

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1.0 Introduction

OASIS is a collection of analysis routines and a Graphical User Interface (GUI) developed for the Cloud Imaging Probes (CIP) manufactured by Droplet Measurement Technologies, Inc.

These probes utilize an illuminated one dimensional photo-diode array to create 2-d

“shadow” images of cloud particles which pass through the sample area. OASIS supports both 1-bit (Mono) and 2-bit (Grayscale) CIP data formats obtained from the DMT PADS acquisition systems. OASIS has been developed to operate on multiple CPU cores/threads simultaneously, speeding up data processing and analysis.

1.1 OASIS Data Format Compatibility

OASIS is compatible with the following data formats:

 PADS/M300 CIP-Mono

 PADS/M300 CIP-Gray

2.0 Installing OASIS

OASIS has been developed within IGOR Pro, a scientific graphing and data analysis program available on the Microsoft Windows and Macintosh platforms. If the user does not already have IGOR installed, they can purchase a licensed copy from DMT that will also enable them to run other analysis programs related to the other DMT instruments. In order to use the OASIS package, certain plugins which extend the functionality of IGOR Pro need to be installed. These plugins are referred to as XOPs, due to the file extension. Details of installing the XOPs can be found below. More information on IGOR Pro can be found at the following website:

http://www.wavemetrics.com

2.1 Recommended System Requirements

OASIS has been tested on the following Operating Systems:

 Windows XP Pro

 Windows Vista

 Windows 7

OASIS can also be run on various Linux distributions via the Windows emulator “WINE”.

However, the performance of IGOR Pro (and thus OASIS) when run through WINE is quite poor,

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and so is not recommended. Instead, it is recommended that Linux and Macintosh users run a Windows instance via a virtual machine (e.g. VirtualBox, VMWare), and use this for IGOR Pro and OASIS. The graphical interface for OASIS was designed at a screen resolution of 1920 x 1080, equal to a typical high-definition widescreen monitor. Some distortion may occur at different screen resolutions.

OASIS has the following minimum system requirements*:

 2 GB RAM

 2.0 GHz Dual core CPU

*OASIS can be reconfigured to run on computers with less RAM/CPU power. Contact the vendor for more information.

2.2 Prerequisites

2.2.1 KeyLok drivers

OASIS utilizes hardware protection in the form of a KeyLok encrypted USB dongle. The drivers for this MUST be installed in order to use OASIS. These drivers MUST be installed before the dongle is plugged into the computer. For more information see the KeyLok resources provided with the OASIS package.

Note: Due to limitations with the dongle drivers, only one dongle is recognized by the system at a time. If you are a PADS user and wish to use PADS and OASIS concurrently on the same computer, you will need a modified dongle with both PADS and OASIS key codes on it. Please contact DMT for more information.

2.2.2 IGOR Pro

OASIS operates from within the IGOR Pro program. Users must have a valid copy of IGOR Pro installed, minimum version number v6.22.

2.2.3 PADS Image Data

Note that while you do not need PADS software to run OASIS, OASIS requires input files to be in the format generated by PADS.

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2.3 OASIS Package Installer

2.3.1 Required Files

Table 1 highlights the files which need to be installed for OASIS to operate in IGOR Pro.

Installation can be performed manually by the user (see the IGOR Pro manual for details), or using the installer provided with the OASIS package (detailed below).

Name Source¹ Destination²

OASIS.xop OASIS package IGOR Extensions

HDF5.xop Igor Extensions Igor Extensions

HDF5 Help.ihf Igor Extensions Igor Extensions

HDF5 Browser.ipf WaveMetrics Procedures\File Input Output Igor Procedures

Table 1: Files Required for OASIS to Function within IGOR Pro

1Source files are typically located at: C:\Program Files (x86)\WaveMetrics\Igor Pro Folder

2Destination files are typically located at: C:\Users\<UserName>\Documents\WaveMetrics\Igor Pro 6 User Files.

2.3.2 Running the Installer

(1) Open the OASIS_Installer_v1.pxp file in IGOR Pro

(2) Click the “Install OASIS components” button within IGOR Pro^1,2

(3) A command prompt window should appear. Press any button to kill this dialogue.

(4) OASIS is now installed

2.4 Optional Additional Software: HDFView

OASIS generates an intermediate data file for each raw data file. These intermediate data files are in the HDF5 format (.h5), which is a binary format similar to that of netCDF. The intermediate HDF5 data files contain a variety of single particle/image properties (e.g.

particle area, particle perimeter, particle time stamp). Some users may wish to browse these files. Due to the binary format, browsing these intermediate files is not trivial. A freely available tool, HDFView, is available for download at the following URL. It provides a simple graphical interface allowing users to browse the contents of HDF files.

http://www.hdfgroup.org/hdf-java-html/hdfview/

1 Some installation tasks require IGOR Pro to be closed. Clicking this button causes all open instances of IGOR Pro to be killed.

2 If error messages are printed to the IGOR Pro command history, installation has failed. Contact the vendor for assistance.

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3.0 Starting OASIS

To use OASIS, you must have already performed the following steps, which are discussed in section 2.0 of this manual.

 Install KeyLok drivers

 Install XOP plugins required for IGOR Pro

 Plug the KeyLok dongle into a USB port. To check if the dongle is recognized, click on the “About” button in the upper right of the OASIS window. You will see an error message if the dongle is not being recognized.

To start OASIS, open the file “OASIS_Template_v1.pxt” by double-clicking on it from its folder or, if you are already in IGOR Pro, by using File > Open Experiment. Be careful not to overwrite this file as it represents the starting point for all OASIS activities. After IGOR Pro has finished loading, you will be presented with the OASIS graphical user environment (GUI) as shown in Figure 1. If at this point you are presented with any error messages, the installation of OASIS has been unsuccessful; either check the installation instructions in section 2.0, or contact Droplet Measurement Technologies.

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Figure 1: The OASIS GUI upon Start-Up

4.0 Setting up Input and Output Paths (File I/O Section)

This section of the OASIS GUI establishes paths to the raw data on the hard drive. It also defines a path for any output generated by OASIS, loads PADS .csv data into IGOR, and is used to specify probe/data formats.

4.1 Setting the Data Paths

These controls allow the user to set the input path (the location of PADS raw image data to be loaded) and the output path (the location where the generated intermediate data and images will be stored).

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Set the Input and Output paths using the corresponding Set Path Button , which will present you with a folder selection dialog. See the following figures.

Figure 2: The Set Path Buttons (highlighted in green)

Figure 3: The Dialog Allowing You to Specify the Data Location

Click on the Browse button (highlighted in green in Figure 3).

Figure 4: Selecting the Appropriate Folder

When setting the Input path, this folder should contain the raw data for OASIS to process.

When setting the Output path, this folder can be located anywhere. Users should ensure they have full read/write access to the Output path, and read access to the Input path. The folder selected above is highlighted in red. To accept the chosen folder, click OK.

Set Path Buttons

1. Select folder

2.Click OK

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Figure 5: Accepting the Selected Folder

Figure 6: OASIS Panel with Input Path Displayed

The OASIS panel now displays the Input path. It has also automatically provided information about the data in the Input path in the Data Queue area of the GUI.

The Path Print Buttons print the corresponding Input/Output path to the IGOR Pro command history. This is useful when dealing with long paths that are not fully displayed in the OASIS GUI.

4.2 Viewing Details of Files in Input and Output Directories

The Path Info Buttons create the Input Data Table and Output Data Table with details of any raw/intermediate files in the Input/Output directories.

The Input Data Table (Figure 7) contains information on all files in the current path which are allowed given the currently selected Probe Configuration (namely the filename prefix and suffix; see section 3.2.2). The File OK column refers to the file having an integer number of data buffers, and is useful in identifying corrupt data files.³

3 Corruption of raw data files can occur during transfer via ftp between Windows/Linux operating systems. This corruption occurs when the ftp client assumes the raw data files are ascii, when they are in fact binary. To avoid this problem either (1) correctly configure the ftp client to treat the files as binary, (2) zip/tar raw data files before transferring the data, or (3) use alternative transfer methods.

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Start Date and Start Time specify the starting date and time of data in the file. First Buffer Date and First Buffer Time specify the starting date and time of the first buffer. (A buffer is 4096 bytes of image and image header data. Once a buffer is filled, the probe sends this data to the host software, either PADS or the user’s own software.) Last Buffer Date and Last Buffer Time provide the date of the last data buffer.

Figure 7: Input Data Table

4.3 Specifying the Probe Type

To work correctly, OASIS needs to know details about the instrument(s) that generated the input data. These data includes the probe resolution, the type of imaging (monoscale or grayscale), and the arm width.

In the event you have several probes, you can provide OASIS with details about each probe’s configuration and then select whichever probe generated the data you are analyzing. This selection is made via the Probe drop-down box. You can only process and analyze data from one probe at a time.

Warning: If the probe settings specified in the Probe field and Probe Config table do not match the actual configuration of your probe, OASIS will not work properly.

To modify the probe configuration, click the Edit Probe Config button (see Figure 8).

Figure 8: Edit probe config Button

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The OASIS Instrument table (Figure 9) appears.

Figure 9: OASIS Instrument Table

This table can hold the details for up to 5 unique probes, one per column in the table. Entries in this table are as follows:

Reference: An identifier string used in the Probe Popup Selector.

File Prefix: The prefix for the raw files generated by the probe of interest. See section 4.3.1 for requirements for prefixes. Warning: Improper prefixes can result in incorrect values in the Time Interval field.

File Suffix: The suffix/extension for the raw files generated by the probe of interest. For files with no suffix/extension, this must be entered as “????”, as shown in Figure 9.

Probe Type: Identifies the probe type. M =Mono, G = Gray.

Probe Res: Specifies the resolution of the diode array in units of microns (µm).

Arm Width: Specifies the separation between the probe arms in units of millimeters (mm).

100 is standard, this value can decrease for probes with special Korolev tips.

After you have finished updating the Probe Config table, click on the checkmark icon and then the “x” to save changes. See Figure 10.

Figure 10: Saving Changes to the Probe Config

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4.3.1 Note on File Prefixes

File prefixes should have an underscore at the end of the prefix. There should only be one underscore per prefix. For instance, “Imagefile_” is a good prefix, while “Imagefile_CIP_” or

“ImagefileX” are not.

Following these guidelines will ensure that the Time Interval field (in the Data Queue section) populates correctly.

4.3.2 Troubleshooting Probe Config Issues—Frequently Asked Questions

When I specify new probe config settings, they don’t get saved. Why?

Make sure you are clicking on the checkbox (Figure 10) before closing the Probe Config table.

Also, it’s possible that your settings did get saved, but the OASIS screen hasn’t updated yet.

Select another probe in the Probe dropdown box, then revert to the probe for which you want to process data. The settings should now be updated.

I put in new probe settings, but my OASIS window isn’t updating. What should I do?

See above.

I entered new Probe Config information, and now the values in the Time Interval field look strange. How can I fix this?

Make sure the file prefixes used in the Probe Config settings and in the actual data file names follow the guidelines outlined in 4.3.1.

4.4 Loading PADS .csv data files

Loading PADS .csv files is not required when using OASIS. There are two cases where you may want to load these files, however:

 To use a measured value for True Air Speed, rather than a constant TAS (see section 6.0 for details)

 To graph OASIS-generated variables against PADS output channels (For advanced IGOR Pro users only)

Click on the Load PADS csv button (Figure 11) to load PADS .csv files into OASIS.

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Figure 11: Load PADS csv Button

After clicking this button, use the dialogue to point to the folder of interest. All PADS CIP .csv files are loaded into OASIS, into the PADS data folder, and into an appropriately named sub- folder.

4.4.1 Troubleshooting .csv File Loading

If you get an error message like the one in Figure 12, you may need to rename the PADS .csv file. OASIS expects the file name to be something like 00CIP20080326155045.csv, where the 14 characters preceding the “.csv” denote the date and time (YYYYMMDDhhmmss). If you have added a suffix to your file name or otherwise changed it, OASIS will not be able to extract the starting time stamp from the file name. It will then be unable to properly convert times within the file.

Figure 12: Error Message Displayed When OASIS Encounters an Unexpected Filename

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4.4.2 Viewing Loaded PADS csv Files

After you have loaded PADS csv files, you can examine the data using the Data Browser.

1. On the IGOR Pro Menu, click Data and then Data Browser. See Figure 13.

Figure 13: Opening the IGOR Pro Data Browser

2. Within the pop-up window, click on root:PADS and find the data file you want. Note: If you do not see a PADS directory or the directory is blank, you need to reload the PADS .csv file.

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Figure 14: Locating a PADS Data File within the IGOR Pro Data Browser

Scroll down the channels listed under the data file. To view data for a channel, double-click on the channel name.

4.5 Other Options Related to File Processing (nProc, GZIP, and Overwrite)

OASIS provides several options to allow users to determine how image files are processed.

1. To control processing speed: Processing is resource-intensive and can take a long time.

If you know the number of processors your computer has, you can instruct OASIS how many of these processors should be devoted to OASIS data processing. Selecting fewer processors will decrease the processing speed but increase the CPU available for other computing tasks. The n Proc field (#1 in Figure 15) stores the number of processors to be used in OASIS data processing.

2. To control output file size: You can select the degree of compression to apply to intermediate hdf5 data files via the GZIP field. 0 = no compression, 9 = maximum compression. The default value of 1 is recommended, as it provides considerable compression with minimal CPU overhead.

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3. To set file protections: The Overwrite box determines whether intermediate hdf5 files are protected from being overwritten. (Clear = protected, Checked = unprotected). Note: If the user tries to process a new file to the same location as an existing one, and Overwrite is not selected, OASIS will not process the file.

Figure 15: Other File I/O Options

5.0 Filtering Input Data (Data Queue Section)

The Data Queue (Figure 16) in OASIS is used to specify what data is to be operated on. This data can be filtered by file type and/or by particle type. By default, OASIS processes 1.) all qualified files in the input path and 2.) all particle types.

Figure 16: Data Queue Section of OASIS

The filters specified in the Data Queue section are applied all OASIS operations:

 Data processing

 Image generation

 Data analysis

5.1 Filtering Data Files

5.1.1 Filtering Files by Time Interval

This method specifies the data which will be operated on by the Time Interval string. In order to use and specify this method, the radio button next to Time Interval must be selected. This string has the following format:

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YYYY/MM/DD hh:mm:ss - YYYY/MM/DD hh:mm:ss

Note: For initial image data processing, i.e. that performed by clicking the Process button, DMT recommends that any file filtering be performed using the File List method. If the Time Interval method is used, the specified time boundaries might fall in the middle of a data file.

This in turn results in intermediary HDF5 files that include only a subset of the particle data in the original files, which is not the recommended practice. Once the HDF5 files have been generated, however, you can apply the Time Interval filter during image generation and data analysis.

5.1.2 Filtering Files by File ID or File Name

This method specifies the data which will be operated on by the File List string. In order to use and specify this method, the Radio Button next to the string must be selected. The string can take a number of different forms:

 A list of File IDs*: e.g. “0,1,2,3”

 A range of File IDs*: e.g. “0-3”

 The all keyword: e.g. “all”

 The wildcard keyword: e.g. “Wildcard:Imagefile_20090303*”

*File ID is the integer value that refers to the row number (position) of the file of interest in the Input Data Table (see Figure 7).

5.2 Filtering Particle Types

5.2.1 Defining Categories for Particle Types

When you generate images and analyze data, it is possible to consider only particles satisfying certain criteria or “filters.” Several sets of criteria can be stored to allow you to quickly switch between particle acceptance criteria. The details of the rules being applied can be found in the OASIS Particle Category Table (Figure 17).

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Figure 17: OASIS Particle Category Table

The Particle Category Table can be accessed by clicking on the Particle Category button.

Details of the rules dictated by this table are found in Appendix A.

Note: Any modifications to Category 1 will have no effect on filtering. This is because Category 1 is reserved for “no filtering” or all particles. The other entries (category 2-5) can be edited freely. Entering illegal characters into the Particle Category Table will result in OASIS disabling several features.

5.2.2 Selecting a Particle Category to Use as a Filter

Once you have defined particle categories, you can select a category to act as a filter. Do this by selecting the respective Reference from the Category drop-down box. In Figure 18, for example, the “round” category has been selected.

Figure 18: Selecting a Category

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6.0 Setting True Airspeed (TAS Data Section)

6.1 Why Airspeed Matters

The True Airspeed (TAS) or Probe Airspeed (PAS, the term used in PADS 3) is very important.

This variable determines the probe sample volume which is used in the Data Analysis section.

Also, the airspeed at the time of acquisition must be the same as the actual airspeed, otherwise the assumption of square pixels in images breaks down. This can lead to incorrectly sized particles and skewed shape factors.

Users have two basic options for setting TAS: using a constant value or using measured TAS data from a file.

6.2 Using a Constant TAS

For a quick look at the data, a constant airspeed can be sufficient.

 Ensure the const radio button is selected (Figure 19)

 Enter the value of the airspeed (ms^-1) in the Default TAS box

Figure 19: TAS Data Section with a Constant Airspeed of 100 m/sec Selected

6.3 Using Measured TAS Data from a File

6.3.1 Identifying an Appropriate Source for Measured Air Speed Data

Potential sources of measured air speed data include the CIP/CAPS on-board pitot tube, as recorded in the PADS .csv files, or the airspeed recorded on a core aircraft system. The air speed source should be whatever the user feels most accurately represents the airspeed experienced within the probe sampling region.

Air speed data must include two variables, Speed and Time. Speed is the air speed in m/sec, and Time is the time in seconds for each TAS data point. The data pointed to in the Speed and Time fields can come from any data source. However, Time must use the IGOR Pro convention, which includes the contribution from the date (see section 6.4). If you have loaded PADS .csv files, the times will automatically be in the correct format.

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6.3.2 Specifying PADS Channels as Sources for TAS

If you have loaded PADS .csv files (see section 4.3.1), the channels in these PADS files are available to be used as sources for Speed and Time. To specify PADS channels as sources, follow the instructions below.

1. In the TAS section, click on the other radio button. This will enable the Actual Speed and Actual Time dropdown boxes. (Logged Speed and Time are not functional at this time.)

2. Click on the arrow to the right of the In the Speed box (Figure 20). Then select

“Browse” from the drop-down menu.

Figure 20: Clicking on Arrow to Right of Speed Box

3. OASIS will display a window allowing you to navigate to the PADS file (Figure 21).

Select the file you would like to use as a source. You may need to expand the contents of directories by clicking the “+” signs.

Figure 21: Selecting PADS File for TAS Source

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4. If you have not already done so, expand the contents of the file by clicking the “+”

icon next to the file name. You should now see the channels displayed underneath the filename, as Figure 21 shows. Select the channel you would like to use for speed (Figure 22) and click OK.⁴

Figure 22: Selecting PADS Channel for TAS Source

Repeat steps 2-4 with the Time field to select the time source. The Time channel should appear near the top of the channel list and be named something like “TimeW.” When the PADS csv files were loaded into OASIS, they were reformatted to use the IGOR Pro standard.

Thus you should not need to reformat the time as described in section 6.4.

6.3.3 Specifying Other Sources for TAS Data

Importing data from other sources such as binary formats (e.g. netcdf and hdf) is possible but not in the scope of this manual. Refer to the IGOR Pro user manual or ask the vendor for support.

Note that for OASIS to work properly, any imported Time data must be in the IGOR Pro Time format. See section 6.4.

4 These channel names can differ for different versions of PADS. In PADS 3, for instance, the True Air Speed channel became Probe Air Speed (PAS). Consult the PADS manual (DOC-0116 for PAD 2 or DOC-0300 for PADS 3) if you are unsure which channels to use.

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6.4 Time Format in IGOR Pro

OASIS uses the time convention native to IGOR Pro: all times are reported as the number of seconds since midnight on 01/01/1904. If you are using an external data source for TAS Speed and Time, rather than a constant TAS or uploaded PADS csv data, you will need to apply an offset to account for the date. It is recommended that you use the internal IGOR Pro function date2secs(year, month, day) to obtain this offset.

Example: Say you have a wave in IGOR Pro called TimeW, which for this example contains the time data in seconds-since-midnight format. You wish to add the date offset for 23^th March 2008. In the command line, you would type the date2secs command line as shown in Figure 23.

Figure 23: Adding Time Correction in IGOR Pro's Command Line

You can verify that the wave was successfully reformatted using the data browser. On the IGOR Pro Menu, click Data and then Data Browser. Click on the root directory (Figure 24) and navigate to the file where the channel is located. Then double-click on the channel name to inspect the contents.

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Figure 24: Root Directory in Data Browser

It is recommended that time data is stored in double precision floating point waves to avoid truncation errors. To change an existing wave into a double precision floating point wave, use the Redimension/D command (Figure 25). The Redimension/D command should be done before adding date2secs to the Wave. See the IGOR Pro manual for more on using Redimension. You may also need to expand the number of digits displayed in the Data Browser. You can do this by right-clicking on the table displaying the wave, then selecting

“Digits” and selecting a larger value (Figure 26).

Figure 25: Entering the Redimension Command

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Figure 26: Expanding the Digits Displayed in the Data Browser

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7.0 Generating Intermediate HDF Files (Raw Data Processing Section)

7.1 What the “Process” Button Does

Data Processing in OASIS refers to the act of opening a raw data file, loading raw data, decompressing the raw data, extracting the 2d images, calculating various properties of the 2d images, and saving these properties to intermediate HDF (.h5) files.

7.2 Processing Options

OASIS includes several options to process different components of the raw data:

 Index Buffers – extract the timestamp data saved with each data block.

 Index Particles – extract single-particle time stamps

 Analyze Particles – extract single-particle properties (area, perimeter, etc.)

Figure 27: Options for Raw File Processing

It is recommended all three components are selected by the user as they are necessary for graphing and statistical analysis.

7.3 Starting and Aborting Processing

In order to start processing, click the Process button. OASIS will start processing the data in the Data Queue. There is a small spinning wheel in the bottom left of the IGOR window that lets you know the data are being processed.

Figure 28: Abort Button

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Warning: The Time Remaining indicator and the red bar may not update immediately, even though the wheel is spinning. In most cases waiting will resolve the issue. If these indicators have not updated in several minutes, however, you may have the wrong instrument selected in the Probe field. For example, CIP-GS may be selected when the image data file is from a CIP monoscale update. In this case, you must abort processing, change the Probe type, and reprocess.

To abort processing, click on the Abort button next to the spinning wheel. You may see the following error message, which will be removed in an upcoming version of OASIS. This does not indicate a problem with the program or experiment.

Figure 29: Error Message after Processing has been Aborted

After aborting, click on the red “Clean-up” button in the lower right corner of the OASIS window. This will close all open files and kill open threads associated with the file processing.

8.0 Generating Images (Image Output Section)

Images can be generated from OASIS in a variety of formats (png, pdf, etc.) A subset of the particles can be exported via the use of the Time Interval and Particle Category controls found in the Data Queue fields; see section 5.0. Images are saved in the Output Path.

8.1 Requirements

To generate images, OASIS requires HDF (.h5) files in the output directory. These are generated during raw file processing.

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8.2 Setting Parameters for Image Output

The Image Output section of the OASIS window, shown in Figure 30, allows the user to do the following tasks:

 Specify the colors for grayscale images with the L1, L2, and L3 drop-down menus

 Specify the file type of the generated image with the Format drop-down menu

 Specify the number of slices to display in each set. See section 8.3 for explanations of slices and sets.

 Specify the number of sets of images to display in each image

 Start generating images by clicking on the Output button

Figure 30: Image Output Controls

After you are done setting the Image Output parameters, click the green Output button.

Section 8.4 describes what happens during the image generation process.

8.3 Definitions: Slices and Sets

A “slice” is defined as the state of the probe’s 64-element linear array at a given moment in time. See Figure 31.

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Figure 31: A Particle Slice

Particle images are reconstructed from individual slices. A slice must be stored each time interval that the particle advances through the beam a distance equal to the resolution of the probe. See DOC-0028, the CIP Operator Manual, for more details.

A “set” is a horizontal strip of particle images within the overall image OASIS generates.

Figure 32 displays 20 sets of particle images, with each set consisting of 1300 slices.

Figure 32: Example Grayscale Images Generated by OASIS

8.4 What the “Output” Button Does

When the user presses the green Output button, OASIS begins processing images from the .h5 files. Within OASIS, the images are displayed in a dynamic window entitled

“OASIS_Images:ImageStackWv.” This window continuously updates at the image files get processed.

In the output directory, OASIS records the static image files in whatever format the user has selected—.png, .jpg, etc. Each .h5 file typically yields many static image files. Note that within these files, image sets are presented in reverse chronological order; see Figure 32.

Image generation can be terminated by clicking on the Abort button (Figure 28).

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9.0 Graphing and Data Analysis (Data Analysis Section)

OASIS contains analysis tools that reduce the single-particle data in the HDF files into derived data products (multi-dimensional waves, graphs, etc.). OASIS can generate a variety of 1-d and 2-d data products on user-defined grids in both logarithmic and linear space.

9.1 Requirements

To analyze data and generate plots, OASIS requires HDF (.h5) files in the output directory.

These are generated during raw file processing.

9.2 Overview of Data Analysis Parameters

To create a new data product in OASIS, you will need to enter the Data Analysis parameters and then click Go. See below for more information on the Data Analysis parameters.

Figure 33: Data Analysis Parameters

Number on Figure 33

Parameter Definition

(1) Reference The name of the generated data product, e.g. “Conc Plot.” This name will overwrite any pre-existing waves, so be careful with your choice.

(2) Plot checkbox A box that when checked instructs OASIS to generate a plot.

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Leaving the box clear causes the data products to be created, but not a new graph. If the data products are already displayed in a graph, however, this figure will be updated. In this case, leaving the box clear is useful, as it allows users quickly examine the impact of different processing options on the same data product without creating many graphs.

(3) Plot xyz

parameters

See section 9.3 and 9.4 (4) Axis options See section 9.5.

(5) Analysis options See section 9.6.

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Time Interval and File List (in Data Queue section)

Fields that define the data to be analyzed. The user can use these fields to create filters; see section 5.0.

(7) Go button A button that starts the data analysis.

Table 2: Parameters that Affect Data Analysis

9.3 One-Dimensional Plots—f(x) Plots

OASIS can create one-dimensional data products that plot one variable as a function of another. For example, particle number concentration can be plotted against particle size. To produce an f(x) plot and/or data products:

1. From the z dropdown menu, select “n/a”

2. Select the parameter of interest (particle number concentration, e.g.) from the x dropdown menu

3. Select the parameter of interest (particle size, e.g.)from the y dropdown menu

9.4 Two-Dimensional Plots—f(x,y) Plots

Two-dimensional data products can be created, allowing one variable to be plotted as a function of two others. For example, particle number concentration as a function of size and time. In order to produce an f(x,y) plot and/or data products, select the waves of interest from the dropdown boxes for the x, y, and z axes. See (3) in Figure 33.

9.5 Setting the Axis Options

The axis options (see (4) in Figure 33) determine how data are binned in plots—the minimum and maximum values on axes, the resolution of the plot, and whether a log or linear scale is used. Once you select x, y, and the optional z parameters, OASIS will auto-fill the axis option parameters. You can then adjust these as desired. Note that when time is a selected parameter, Max and Min auto-fill to -1. This should not be edited. Rather, times should be edited in the Data Queue section (see section 5.0 of this manual).

Axis options (Min, Max, log, and δ) must be defined for each binning variable. For f(x) operations, you must specify these options for the x data. For f(x,y) operations, you must

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specify this for the x and y data. Note y-axis parameters are grayed out when creating f(x) data, as they are not used to create bins.

9.5.1 Definitions of Axis Options (Min, Max, Log, and Delta)

Option Definition

Min The lower limit of the smallest bin Max The upper limit of the largest bin δ (Delta) Either:

 The spacing between each bin (if Log box is unchecked), or

 The number of total bins (if Log is checked) x Log, y Log,

z Log*

Indicators of whether bins should be spaced linearly or logarithmically:

Linear (box unchecked): Bins are spaced linearly, with constant spacing defined by the δ parameter corresponding to the relevant axis

Logarithmically (box checked): Bins are spaced logarithmically, with the δ parameter now defining the total number of bins.

Table 3: Definitions for Min, Max, δ, and Log Parameters

*Note it is possible to log the color scale of f(x,y) plots using the z log axis checkbox.

9.6 Analysis Options

Depending on the data products being created, a number of optional processing techniques can be applied. These are described in greater detail in Appendix A.

9.6.1 Sizing Options

The Size dropdown menu allows the user to choose the sizing metric used to characterize the particle size. Available options are shown in Table 4.

Menu Entry Details

X Maximum particle width (measured parallel to the array) Y Maximum particle length (measured perpendicular to the array) Mean(X,Y) Mean average of X and Y, i.e. (maximum width + maximum length)/2 Max(X,Y) Largest value of X and Y

Area Equiv. Diameter of a circle with same projected area as the image Proj. Length Length of diagonal inside the bounding box defined by X and Y Table 4: OASIS Options for Particle Sizing Metrics

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Figure 34: Max Width, Max Length and Projected Length

9.6.2 Options for M-2-D (Mass-Diameter) Relationships

The M-2-D dropdown menu allows the user to choose a mass-diameter relationship for the use in estimates. The two options are as described below. In general, “Liquid Sphere” option is best for clouds that consist primarily of water particles, whereas “Brown and Francis” is better for clouds with higher ice content.

9.6.2.1 Liquid Sphere

This option calculates mass in grams from particle diameter, d, in µm as follows:

Mass = Density of Water * Volume of spherical particle * Conversion factor

=

9.6.2.2 Brown and Francis

This option calculates mass in grams from particle diameter, d, in µm as follows:

If d < 100:

Mass = 4.82 x d³ x 10^-13 If d >= 100:

Mass = 7.38 x d^1.9 x 10^-11

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The theoretical basis for this formula is derived from Brown, P. R. A. and P. N. Francis, 1995, Improved measurements of the ice water content in cirrus using a total-water probe, J.

Atmos. Oceanic Technol, 12:410–414.

9.6.3 Sample Area (SA) Options

The SA dropdown menu allows the user to choose a sample area definition. Specifically, it sets the method for determining sample width, or the width of the diode array.

Available options for setting sample width are shown in Table 4.

Menu Entry Calculation used for Sample Width R = Probe Resolution

D = Particle Diameter

Comments

All-in ((64 x R) – D) x 10^-4 Most accurate sizing method for sized particles, but many particles are rejected Centre-in (64 x R) x 10^-4 Sizes most particles, but some particles

are sized inaccurately. This is a frequently used method.

Reconstructed⁵ ((64 x R) + 2((D/2 – D/7.25) x 10^-4) Useful in water clouds, not useful in ice clouds. Good for lots of big spherical particles.

Table 5: OASIS Options for Sample Width

9.6.4 Depth of Field Corrections

This parameter enables the user to apply depth-of-field corrections. Specifically, it applies the Korolev correction to water droplets that fall outside the instrument’s depth of field. This prevents images from appearing oversized and transparent in the center (Korolev, 2007).

9.7 Examples

Below are several examples of the set-up used and the graphs produced using OASIS data analysis.

9.7.1 Inter-arrival times

This example (Figure 35) plots Number Concentration (NConc) in different inter-arrival time (IAT) bins. The 60 bins are log spaced, as indicated by the δ and x log parameters. They span a range from 0.1 µs (min) to 1 second (max). The particle size metric is the max X dimension,

5 This function is described in Heymsfield, Andrew J., Joanne L. Parrish, 1978. A Computational Technique for Increasing the Effective Sampling Volume of the PMS Two-Dimensional Particle Size Spectrometer. J. Appl. Meteor., 17, 1566–1572.

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as indicated by the X in the Size field. The sample area (SA) used is the Centre-in method.

Generated waves are named “IATPlot_x” and “IATPlot_y,” as per the Ref string.

Figure 35: Configuration to Generate Simple IAT Analysis Graph

The set-up shown in Figure 35 yields the following plot.

Figure 36: Number Concentration as a Function of Particle Inter-arrival Time (IAT).

9.7.2 Number Concentration as a Function of Size and Time

This configuration (Figure 37) plots Number Concentration (NConc, z) as a function of both Time (x) and Size (y). The time range is specified by the Data Queue (see section 3.3). The time bin resolution is 1, corresponding to a 1Hz data product. The size range of interest is from 15-1000 µm, with each bin 15 µm wide. (In this example, y’s δ field indicates the spacing between bins rather than the number of bins, because y is scaled linearly.) Particle size is calculated from the Mean of the X and Y measurements. The sample area is calculated using the Centre-in method. Generated waves are named “NumPlot_x,” “NumPlot_y” and

“NumPlot_z,” as per the Ref string. The color (z) scale has log spacing.

50

40

30

20

10

0 Num. Conc. (L-1 )

10^-7 10^-6 10^-5 10^-4 10^-3 10^-2 10^-1 10⁰ IAT (s)

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Figure 37: Configuration to Generate Simple Number Concentration as a Function of Time and Size

This set-up generated the plot in Figure 38.

Figure 38: Number Concentration as a Function of Time and Particle Size

10.0 Exporting Data from OASIS

Generated data products can be exported from OASIS to allow users to distribute data, or perform further analysis in a package of their choice. Currently OASIS can export data in the following formats:

 HDF5

 Tab-delimited text

To export data, enter the full path to the data which is to be exported in the Export Data Wave box. This can consist of a comma separated list of paths to output multiple parameters into a single file. Select the format for the output file from the Format dropdown box, then

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click on the Export button to export data to a file. This will bring up a dialog for you to specify the location for the outputted data file.

Figure 39: Export-Data Options in OASIS

The data product derived, NumPlot_z, is pointed to by the Waves string (root:OASIS:NumPlot_z). The file format is specified to be tab delimited text. Clicking the Export button brings up the dialog shown in Figure 40.

Figure 40: Dialog to Specify File Name and Destination for Exported Data

Warning: If you are exporting Time data, the exported data will have the IGOR Pro time format of seconds since midnight on 01/01/1904. For example, exporting the wave on the left in results in the .txt file shown on the right (opened here in Excel).

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Figure 41: A Time Wave in the IGOR Pro Data Browser (left) and the Corresponding Exported Data in a Tab- Delimited Text File (right).

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Appendix A: Image Processing Description

The operating principles of the CIP are described in the operations manual of this instrument and the details of how the image data is taken and encoded will not be described here. The DMT “Data Analysis Users’ Guide: Chapter II” (downloadable from the DMT website, www.dropletmeasurement.com) describes the CIP’s operating principles, as well, and in addition describes in detail how to analyze image data. Parts of that manual will be repeated here in order to help the user of OASIS choose which options to select when running the routine.

OASIS reads the compressed image files, decompresses them and calculates each individual image’s area, perimeter, maximum length, maximum width and projected length, as well as additional image properties and average statistical bulk properties. Figure 42 illustrates how the dimensions are determined.

Figure 42: Particle Size Derivations Generated by OASIS

Maximum Width This is the dimension labeled ‘Width’ in Fig. A.1. The width is the maximum number of diodes shadowed for any slice while the image is passing over the array, where a slice is a single measurement of the ON/OFF state of the 64 photodiodes in the array.

Maximum Length This is the dimension labeled ‘Length’ in Fig. A.1 and is measured by counting the number of slices and multiplying by the resolution of the probe.

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Projected Length This is also called ‘Projected Diameter’ (Heymsfield et al., 2002) and is calculated as the hypotenuse of the triangle formed by the maximum width and length, i.e.

Dproj = (W² + L²)^1/2

where W and L are the maximum width and length, respectively.

Particle Area If SA is set to “All-in” or “Centre-in,” the area of a particle is calculated by multiplying the number of shadowed pixels by the square of the resolution. If SA is set to

“Reconstructed,” the area is calculated using the method outlined in Heymsfield and Parrish (1978b as listed in the following references). See equations 13 and 16.

Perimeter The perimeter is estimated by summing all of the transitions from ‘ON’ to

‘OFF’ of the pixels, dividing by √2 and multiplying by the resolution. The calculated perimeter includes any gaps or ‘holes’ inside the image.

Minimum interarrival time (IAT), in microseconds for breakup detection

Ice crystals that strike the tips of the CIP will sometime shatter, depending on their size and habit, producing a small cloud of fragments. Some of these can be rejected if their time arrival, a measured parameter, is very short (Field et al., 2006). Selection of this parameter requires some trial and error, i.e. if selected too short, some shattered fragments will be erroneously accepted but if selected too long, some good particles will be rejected. One approach is to first run OASIS with this parameter set to zero. Then process the particle by particle file (PBP, see description below) and generate a frequency histogram of the elapsed time (see DMT Data Analysis Manual, Part II). Inspection of this histogram will usually allow optimum selection of the minimum arrival time to reject the shattered fragments.

Maximum allowable length to width ratio (streaker filter)

The tips of the CIP are designed to minimize the impact of water that sheds when flying in heavy liquid water; however, there can sometimes be this type of shedding that is unavoidable. The symptom is a very elongated image where the length is several times that of the width. The user can adjust this and see how the resulting size distributions are impacted.

Maximum allowable area ratio (shatter spray detection)

Another symptom of shattering or drop sprays when a large crystal or raindrop strikes the probe tip will be many small images within a single image frame (see DMT Data Analysis Manual, Part II). These can be rejected by looking at the ratio the maximum area to the measured area. The maximum area is that of the rectangle that encloses the maximum width and length and the measured area is just the sum of all the shadowed pixels, as defined previously. A spray of particles produces a lot of small, shadowed pixels, not necessarily connected to one another but creating what appears to the CIP processing electronics as a single image. The area ratio will usually be larger than about 4 under these conditions.

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Korolev correction flag

Particles that pass through the CIP laser beam at a distance farther from the center of focus than their optimum depth of field (DOF) will form an image that is usually larger than the particle size and will also look like they have a transparent center (Korolev, 2007). If the user selects “Korolev” in the DoF Corr. field, OASIS will correct images for water droplets that have these size and transparency issues.

Sample Area Flag: 0=All in, 1=Center in

The calculation of number concentration, liquid/ice water content, rain rate and reflectivity all require that the number and size of cloud particles are calculated as a function of a unit volume of air. This volume is the product of the area swept out per unit time. The area swept out is the product of the sample area, calculated as the DOF times the effective array width, the airspeed and the sample time (see DMT Data Analysis Manual, Part II). There are two ways to calculate the effective array width (Heymsfield, and Parrish, 1978a,b). One method rejects any particle that shadows one or both of the array end diodes (All-In method) while the other assumes that the center of the particle is within the array (Center-In). The All-in method assures that no partial images are incorrectly sized; however, this restricts the sample volume and requires longer sample times to acquire good statistics. The center-in technique provides a larger sample volume but might derive the size incorrectly. The default is 0, or all-in.

Diameter definition:

When measurements are made in liquid water clouds, the definition of the “diameter” of a particle is obvious; however, in ice or mixed phase clouds, the term “diameter” is no longer a correct definition yet to create a size distribution we need some description that is meaningful. The scientific community has not reached a consensus, but the most commonly used derivations of size are Maximum Diameter, calculated as the maximum width or length, Projected Diameter (see Figure 42) proposed by Heysmfield et al. (2002) and the Area Equivalent Diameter, the diameter of droplet with the measured area of the image (Baker and Lawson, 2006; Lawson and Baker, 2006).

Area to Perimeter^2 ratio tolerance

Numerous methods have been published for identifying cloud particle habits. The simplest is to distinguish round images from those that are not round. This is done by comparing the area to perimeter squared ratio of a circle (0.079) to that of the measured image. Due to the resolution of the probe and pixelizing of the image, the ratio computed from the measurements will not be exactly that for a circle when water droplets are measured. Hence, this parameter is used to provide a little flexibility when trying to separate water droplets from ice crystals. The default value is 0.9.

Ice Crystal Density to use

Optical Array Shadow Imaging Software (OASIS) 1.0