chemdata:digitizer

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chemdata:digitizer [2014/02/14 15:12]
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chemdata:digitizer [2017/08/17 10:00] (current)
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-===== Mass Spectrum Digitizer Program ===== +===== Using the NIST Spectrum Digitizer Program =====
-Written by Meng Zhai +
-Chemical and Biochemical Reference Data Division +
-National Institute of Standards and Technology (NIST), Gaithersburg,​ Maryland+
  
-For inquiries regarding this program please contact Dr. David Sparkman at odspark@gmail.com. ​+Written by Meng Zhai \\  
 +Chemical and Biochemical Reference Data Division \\  
 +National Institute of Standards and Technology (NIST), Gaithersburg,​ Maryland \\
  
-Download the program [[http://​chemdata.nist.gov/​mass-spc/​digitizer/​downloads/​SpectrumProgram.jar|here]] (1/8/2010). 
  
-==== Short tutorila ==== +For inquiries regarding this program ​please contact DrDavid Sparkman at ods@csi.com.
-The following is a tutorial on how to digitize a mass spectrometry spectrum using the Spectrum Digitizer ​program. ​There are step-by-step instructions on how to go from an image to a .msp file containing the desired information+
  
-{{:chemdata:initial.jpg |image of spectrum}}{{:​chemdata:​final.jpg|digitized spectum}}+ 
 +**Download the program** [[http://chemdata.nist.gov/​mass-spc/​digitizer/​downloads/​SpectrumProgram.jar|here]] (1/​8/​2010). 
 + \\ 
 + 
 +The following is a tutorial on how to digitize a mass spectrum using the //NIST Mass Spectrum Digitizer Program//. These are step-by-step instructions on how to go from a graphic ​image to an .msp file containing the desired information. The NIST MS Search Program can then import the .msp file. 
 + 
 +This program requires that Oracle’s Java be installed (https://​java.com/​en/​). Click on the Free Java Download button. 
 + 
 +=== Some Important Information:​ === 
 +Oracle’s Java is already installed on many computers. Download the NIST Spectrum Digitizer Program. This file (**SpectrumProgram.jar**) will be in the \Download folder. When the Mouse pointer is put on the Program’s name and the left Mouse button is double-clicked,​ the Program will run, if Java is installed. If the Program causes a dialog box to be opened that ask for an association,​ it will be necessary to first download and install Java. After Java has been installed, try to run the //​Digitizing Program// again. 
 + 
 +There is no installation and no icon is created for the //​Digitizing Program//. For convenience,​ it may be desirable to move the Program to the folder containing the NIST Library, e.g., \NIST17. It may also be convenient to create a Desktop icon, but the //​Digitizing Program// can always be started from Windows Explorer by putting the Mouse pointer on the name and double-clicking the left Mouse button. 
 + 
 +When a graphic spectrum is imported it may include numeric labels on the X-axis (abscissa) and the Y axis (ordinate) and the tops of some of the peaks. The spectrum ​may have a graphic representation of a structure. None of these annotations are taken into consideration by the Program in the digitizing process. 
 + 
 +When a graphic spectrum is displayed in the Program, it cannot be Closed. Opening a new graphic display will replace the existing display, clear the **Points List** (lower part of the **Vertical Information Column** on the right side of the Program’s desktop), the **X Calibration Points List**, and any **zoom** from the previous display. The spectrum information fields (text boxes at the top of the display) are not cleared when a new spectrum is displayed. It is necessary to put the Mouse pointer on the **Clear** button (one of four buttons on the left side of the top of the desktop, in line with the text boxes) and click the left Mouse button to clear these fields. The **Date:** and **Digitizer:​** fields will not be cleared when the Clear button is selected. The **Date:** field updates automatically. Whatever is in the Digitizer: field remains until changed, even when the Program is closed and re-opened. 
 + 
 +The **Y0:** and **Y1:** fields ARE CLEARED when a new graphics display is opened. The **Left** and **Right** positions and the **Threshold** positions ARE NOT CLEARED. It is best to reset these three positions for each new graphic. 
 + 
 +When the //​Digitizing Program// is closed by putting the Mouse button on the **X** button at the far upper right of the desktop and clicking the left Mouse button, all data is removed. When the Program is started at a later time, the previous data and information will be gone. Only the **Date:** and **Digitizer:​** fields will be populated. The default **File Open** dialog box and the default **File Save** dialog box will point to the folders last used before the Program was last closed. 
 + 
 +When the Mouse pointer is placed on the upper **Reset** button (previously,​ the **Done** button) in the upper part of the **Vertical Information Column** on the right side of the Program’s desktop, and the left Mouse button is clicked, all the values in the **X Calibration Points List** will be cleared and all the **Digitized //m/z// – intensity Pairs List** will be cleared. The affected zoom will remain. The values for **Y0**, **Y1**, **Left**, **Right**, and **Threshold** will be retained. The label on this **Reset** button returns to **Done**. 
 + 
 +When the Mouse Pointer is placed on the lower **Reset** button (previously,​ the **Set Points** button) and the left Mouse button is clicked, only the **Digitized //m/z// value-intensity Pairs** are deleted. The label on this button then returns to **Set Points**. The **Y0** and **Y1** values, **Left**, **Right**, and **Threshold** values and the **X Calibration Points** are not cleared. It is now possible to alter these various parameters to achieve a better digitization. 
 + 
 + 
 +{{ :chemdata:digispectra.png?​nolink ​|Figure 1}} 
 +<WRAP 90% > 
 +**Figure 1.** The NIST Mass Spectrum Digitizer Program Desktop. The vertical red line is used to fix the position of the X points and the Left and Right Boundaries which are indicated by the two vertical-green lines on either side of the spectrum. The horizontal red line is used to fix the Y0 (base line of the mass spectrum) and Y1 (maximum intensity) points and the Threshold, which is indicated by the horizontal turquoise line. 
 +</​WRAP>​
  
 === Obtaining the data === === Obtaining the data ===
-  ​- Opening a spectum + 
-    - Click on the Open button. +The Program will always open with no data loaded. A blank desktop. 
-    - Find your image.You will only be allowed to choose ​images of the supported file types (.jpg, .bmp, .gif, .png). + 
-    - Click on the Open button in the file chooser ​box. Your image should now appear. +  ​**Opening a spectrum** 
-  - Resizing the image +    - Put the Mouse Pointer ​on the **Open** button on the top left of the Program’s desktop and click the left Mouse button. This opens the **File Open** dialog box. The default location is the last folder used before closing the Program or when selecting a previous graphic. Navigate this dialog box in the same way any **File** dialog box is navigated. Once the folder containing the graphic file of the spectrum has been located, Highlight the folder’s name, put the Mouse pointer on the **Open** button, and click the left Mouse button. 
-    - After you open an image, ​you can press the + or buttons ​to zoom in and out on the image. ​Press the Unzoom button to set the image to its original size. +    - Find the desired file, Highlight its nameOnly images of the supported file types (.jpg, .bmp, .gif, and .png) may be selected
-    - After you are satisfied with the size of your image, ​press the Done button to continue. +    - Put the Mouse pointer ​on the **Open** button in the **File Open** dialog ​box and click the left Mouse buttonThe image will appear ​on the Program’s desktop
-    - If you want to go and and change ​the zoom on your image, ​press the Reset button (originally ​where the Done button ​was located).  +  - **Resizing the image** 
-  - Adding X calibration values +    - After an image is opened and displayedit is possible to put the Mouse pointer on the **+** or **–** ​buttons ​under the button labeled **Unzoom** ​in the **Vertical Information Column**, to increase or decrease the size of the image by clicking the left Mouse buttonSmall increments in both the x- an y directions are achieved for each click. Click on the **Unzoom** button to set the image to its original size. 
-    - You will need to give the program some calibration points for it to workThe textbox at the top right corner should say "Set X"+    - After the desired ​size of the image is achievedput the Mouse pointer on the **Done** button and click the left Mouse button to continue. This button will now be labeled **Reset**. All the buttons in the **Vertical Information Column** that were previously grayed and unavailable are not available. The **Unzoom** and **+** and **–** buttons are now grayed
-    - The red crosshairs should ​follow ​your mouse. Move your mouse until the vertical red line is lined up with an X value that you know the real value ofand click to set that value. +    - If the zoom of the image needs to be changedput the Mouse pointer on the **Reset** button (originally ​labeled ​the **Done** button) ​and click the left Mouse button. This will make the **+** or **–** buttons available and the **Reset** button’s label will change back to Done. The image WILL NOT be returned to its original size. It will remain its present side until resized with the **+** or **–** buttons or the **Unzoom** button is selected. This will also delete any **X Calibration Points** and any **Digitized //m/z// value-intensity Pairs**
-    - The "Image X:" value should ​change ​as you move your mouse. This is the pixel value of the X value you click on. Once you clicked your mouse, the textbox next to "Real X:" ​is highlighted. This is where you should enter in the actual X value you have just selected. +  - **Adding X calibration values** \\ It is necessary ​to provide ​the Program with calibration points for the x-axis. As the Mouse pointer is moved over the surface of the display, a vertical and horizontal red line will change locations. It is best to set the **X Calibration Points** before setting the **Y Calibration Points**. 
-    ​Once you have the correct pixel and real values ​for the value you have just selectedclick on the Add button, or press the Enter key on the keyboard. +    - There is a button on the left of the **Vertical Information Column** on the Program’s ​right side labeled **Set X**. Put the Mouse pointer on this button and click the left Mouse button. This button will be grayed until the **Done** button has been selected and is labeled **Reset**. Once the **Set X** button has been selected, **Set X** will appear at the top of the **Vertical Information Column**
-    - The pixel and real value should be added to the calibration listYou can add as many X calibration ​values ​as you wantbut you need to have at least two points. Calibration points are always added to the list in the format: pixel value, real value. +    - The red cross-hairs will follow ​the Mouse pointer as it is moved over the image. Move the Mouse until the vertical red line is lined up with an X value that is a known //​m/​z// ​value in the spectrum. As the Mouse pointer is movedthe value in the box next to the **Image X:** label will change. Click the left Mouse button to lock the value. ​After clicking the left Mouse button, the value in the **Image X:** box will not change. This is the pixel value of the X value that has been selected. 
-    - The program automatically waits for you to click on the next pixel value, so repeat ​steps 1-until you have the desired number of X calibration values. +    - Once the pixel value for X is set, the textbox next to the **Real X:** label is highlighted. This is where the //m/z//-value for X should be typed. After typing ​the //​m/​z// ​value, press the Enter key on the keyboard ​or put the Mouse pointer on the **Add** button and click the left Mouse button. Either action will result in the pixel-//​m/​z//​ value pair being added to **X Calibration Points List**. Once a pixel value is locked, it is necessary to set a value for **Real X:**. Another pixel value cannot be set without setting a corresponding value for **Real X:**.  
-    - If at any time you need to add more X calibration values, ​click on the Set X buttonand then start at step 1.  +    - If an error was made in selecting the pixel value, just enter an //m/z// value and delete ​the pair later. 
-  - Deleting X calibration values  +    - As many X calibration ​pixel-//​m/​z//​ value pairs as desired can be added; however, at least two calibration pairs are required. Calibration points are always added to the list in the format: pixel value followed by the //​m/​z// ​value. 
-    - You can also delete ​calibration ​valuesSelect ​the points ​you want to delete. (You can select ​multiple values by using shift and control.) +    - The program automatically waits for the next pixel value to be selected by positioning the vertical red line and clicking the left Mouse button. Repeat ​steps a)-e) until the desired number of X calibration values ​have been selected. X calibration values appear in increasing pixel-//​m/​z//​ values from top to bottom
-    - Click on the Delete button. Remember, ​you need at least two calibration points to proceed. +    - If at any time it is necessary ​to add more X calibration values, ​put the Mouse pointer ​on the **Set X** button and click the left Mouse button. Then start at step a). 
-  - Calibrating Y0 +    - If the **Set Points** button has been selected and its label has changed to **Reset**, the **Set X** and **Add** buttons will be grayed and unavailable. To add new X calibration points, it will be necessary to put the Mouse pointer on this lower **Reset** button and click the left Mouse button. After the new X calibration point has been added, it will be necessary to use the Set Points button to get a revised digitized spectrum
-    - You will need to also calibrate the Y values ​by setting two points, the minimum and the maximum. To set the minimum, ​click on the Set Y0 button. +  - **Deleting X calibration values**  
-    - The textbox at the top right corner ​should ​say "Set Y0"+    - X calibration points ​can be deleted. If a series of X calibration ​points have just been added, they will appear grayed in the listIf the number of calibration ​points ​exceeds the size of the box, a scroll bar will appear on the right of the box. \\ Before the X calibration points can be deleted, they must be un grayed. This may require putting the Mouse pointer on the **Set Y0** button and clicking the left Mouse button. This is a known bug. \\ Highlight the values ​to be deleted and then put the Mouse pointer on the **Delete** button (located just under the list) and click the left Mouse button. (Select ​multiple values by using the **Shift** ​and **Ctrl** keys on the Keyboard.) 
-    - Move your mouse until the horizontal red line is lined up with the X axis (where Y is 0), and click to set that value. +    - After selecting the points to be deleted, put the Mouse pointer ​on the **Delete** button and click the left Mouse button. Remember, at least two calibration points ​are needed ​to proceed. 
-    - The "Image Y0:" value should ​change as you move your mouse. This is the pixel value of the value you click on. The "Real Y0:" value is set to 0 by default, and it is not recommended that you change ​this value. +  - **Calibrating Y0** \\ There are no graphic indications of the **Y0** and **Y1** values, just as there are no graphic indications as to the position of the **X Calibration Points**. 
-  - Calibrating Y1 +    - The Y values ​will need to be calibrated ​by setting two points, the **minimum** and the **maximum** peak intensity. To set the **minimum**put the Mouse pointer ​on the **Set Y0** button and click the left Mouse button. 
-    - You will need to input the maximumY1. Click on the Set Y1 button. +    - The textbox at the top of the Vertical Information Column ​should ​now read **Set Y0**
-    - The textbox at the top right corner should ​say "Set Y1"+    - Move the Mouse until the horizontal red line is aligned ​with the X axis (where Y is 0 is), and click the left Mouse button ​to set that value. 
-    - Move your mouse until the horizontal red line is lined up with the top of the highest ​peak on the spectrum (the maximum Y value), and click to set that value. +    - The text value in the box next to the **Image Y0:** label will change as the Mouse is moved. This is the pixel value of the selected Y0 value and is locked when the left Mouse button is clicked. The value in the box next to the **Real Y0:** label is set to 0 by default, and it is recommended that this value not be changed
-    - The "Image Y1:" ​value should change as you move your mouse. This is the pixel value of the Y value you click on. The "Real Y1:" ​value is set to 9999 by default, and it is not recommended that you change ​this value. +  - **Calibrating Y1** 
-  - Setting the boundaries and getting the data +    - The maximum Y1 value needs to be setPut the Mouse pointer ​on the **Set Y1** button and click the left Mouse button. 
-    - You will also need to set boundaries on your spectrumClick on the Left button. +    - The textbox at the top right corner should ​read **Set Y1**
-    - The textbox at the top right corner should ​say "Set Left Bound"(When you set the right bound and the threshold, the text in the box should change accordingly.) +    - Move the Mouse until the horizontal red line is aligned ​with the top of the most intense ​peak on the spectrum (the maximum Y value), and click the left Mouse button ​to lock this value. 
-    - Move your mouse until the vertical red line is where you want the left boundary ​to be, and click to set the boundary. The program will not get any data to the left of this line. +    - The box next to the **Image Y1:** label will contain the pixel value for Y1. This is the pixel value for Y value selected. The box next to the **Real Y1:** label value is set to 9999 by default, and it is recommended that this value not be changed
-    - You will also need to set the right boundaryClick on the Right button. +  - **Setting the boundaries and getting the data** 
-    - Move your mouse until the vertical red line is where you want the right boundary ​to be, and click to set the boundary. The program will not get any data to the right of this line. +    - The boundaries (lowest and highest //m/z// values that an intensity can be observed in the digitized spectrum) of the spectrum ​will need to be set. Put the Mouse pointer ​on the button labeled **Left** (lower part of the **Vertical Information Column**) and click the left Mouse button. 
-    - You will also need to set the X threshold. The program will not get any data that has peaks below this line. Click on the Threshold button. +    - The textbox at the top right corner should ​read **Set Left Bound**. When the **Right** button is selected to set the right boundary, the text in this box should change accordingly. 
-    - Move your mouse until the horizontal red line is where you want the threshold line to be, and click to set the threshold. Make sure the line goes through all the peaks you want and above any peaks you don't want, since the program will not get any data that has peaks below this line. +    - Move the Mouse until the vertical red line is where the left boundary ​should ​be, and click the left Mouse button ​to set the boundary. The program will not get any data to the left of this line (a green vertical line on the left side of the display)
-    - When you are satisfied with the three boundaries ​you set and all your calibration values, ​click on Set Points to get the data. +    - A right boundary ​will also need to be set. Put the Mouse pointer ​on the **Right** button and click the left Mouse button. 
-  - Viewing the data +    - Move the Mouse until the vertical red line is where the right boundary ​should ​be, and click the left Mouse button ​to set the boundary. The program will not get any data to the right of this line (a green vertical line on the right side of the display)
-    - After click on Set Points, if there had been no errors, a list of all the data points of real values, in the format ​x,y, should ​appear in the list in the bottom right hand cornerPink and green points should also be drawn on the peaks in the spectrum image. Each of the points drawn corresponds to a point in the list.+    - An X threshold value will need to be set. The program will not get any data that has peaks below this line (a vertical turquoise colored line)Put the Mouse pointer ​on the **Threshold** button ​and click the left Mouse button. The top of the **Vertical Information Column** will read **Set Threshold**
 +    - Move the Mouse until the horizontal red line is where the threshold line should ​be, and click the left Mouse button ​to set the threshold. Make sure the line goes through all the peaks to be included in the digitized spectrum ​and above any peaks that are to be excluded because ​the program will not save any data that has peaks below this line. 
 +    - When all three boundaries ​have been set and all calibration values ​are correctput the Mouse pointer ​on the **Set Points** button and click the left Mouse button ​to get the digitized ​data. The label on the **Set Points** button changes to **Reset**. Placing the Mouse pointer on this lower **Reset** button and clicking the left Mouse button results in all the digitized points being deleted. The **Y0**, **Y1**, **Left**, **Right**, and **Threshold** values remain. They can be changed. When this **Reset** button is selected, the label on the button changes back to **Set Points**. The X Calibration Points are unaffected by the selection of this Reset button
 +  - **Viewing the data** 
 +    - After putting the Mouse pointer ​on the Set Points ​button and clicking the left Mouse button, if there has been no errors, a list of all the data points of real values, in the x (//m/z// value),y (relative intensity based on a scale of 10,000) format will appear in the list in the Digitized //​m/​z//​-intensity Pairs List in the Vertical Information ColumnAlternating pink and green squares (pointsshould also be shown on the top of each peak in the graphic ​spectrum image. Each of the points drawn corresponds to a pair in the list.
  
 === Manually manipulating the data === === Manually manipulating the data ===
-  - Moving points +  - **Moving points** 
-    - Click on a data point in the list to select it. Then, use the arrow keys on the keyboard to move it around+    - Put the Mouse pointer ​a data point in the Digitized //​m/​z//​-intensity Pairs List and click the left Mouse button ​to select it. Then, use the arrow keys on the keyboard to change the values (**Left** and **Right** arrows to reduce or increases the //m/z// value, **Up** and **Down** arrows to increase or decrease the intensity)
-    - Alternatively, ​click on the point you wish to select on the spectrum image, and drag the mouse to move it+    - Alternatively, ​put the Mouse pointer ​on the point in the spectrum image that is to be changed, and drag the Mouse pointer while holding down the left Mouse button ​to move the point
-    - The point that is being moved should ​change coordinates in the list as you move it. +    - The point that is being moved will change coordinates in the list as it is moved. Several clicks of the **Up** and **Down** arrows will be required to change an integer //m/z// value
-  - Adding points +  - **Adding points** 
-    - Click on the Add button. +    - Put the Mouse pointer ​on the **Add** button and click the left Mouse button. 
-    - Click on the spectrum image where you wish to add the point. +    - Put the Mouse pointer ​on the spectrum image where the point is to be added and click on the left Mouse button. When the point is first added, it will be represented on the graphic display of the spectrum by a slightly larger point than those set by the Program. This new point will be colored dark-blue
-    - The new point should appear in the list in the correct, sorted position. +    - The new point should appear in the list in the correct, sorted-position ​with the appropriate intensity. 
-  - Deleting points +    - The Add button must be selected for each and every point that is to be added. When the Add button is selected again, the just added point will be smaller and represented by the alternate green and pink colors used for the other points
-    - Click on the point you wish to select ​on the spectrum ​image to delete+  - **Deleting points** 
-    - The point you selected should also be highlighted in the list. +    - Put the Mouse pointer on the **Delete** button and click the left Mouse button. 
-    - Alternatively, ​you can select ​the point you wish to delete by clicking ​on the data point in the list. +    - Put the Mouse pointer ​on the point to be delete ​on the graphic display of the spectrum to be deleted and click the left Mouse button. The point will be slightly large and its color will be dark-blue.  
-    - Click on the Delete button.+    - The point selected should also be highlighted in the list. 
 +    - Alternatively, ​put the Mouse pointer on the point to be deleted in the **Digitized //​m/​z//​-intensity Pairs List** and click the left Mouse button ​on the data point in the list. 
 +    - Then put the Mouse pointer ​on the **Delete** button ​and click the left Mouse button and the point is deleted.
  
 === Exporting the data === === Exporting the data ===
-  - Entering identification information // +Information ​about the molecule/​spectrum ​can be entered ​in textboxes at the top of the Program’s displayPut the Mouse pointer in the box where information is to be added and click the left Mouse button. Type the desired information. Press the Enter key or move the Mouse pointer to another box. It is best to use the Clear button to clear these fields before starting to add new data. 
-You can enter in information ​about the molecule/​spectrum in textboxes at the top. + 
-    - Name: Name of the molecule. +  - **Entering identification information** ​ 
-    - Formula: The molecular formula of the molecule. +    - **Name:** Name of the molecule. 
-    - MW: The molecular weight of the molecule. +    - **Formula:** The molecular formula ​(elemental composition) ​of the molecule. 
-    - Contributor:​ The author, title, volume/​issue,​ pages, etc. of the journal article that had the spectrum, or the source of the spectrum. +    - **MW:** The molecular weight ​(nominal mass) of the molecule. 
-    - CASNO: The unique CAS (Chemical Abstracts Service) registry number assigned to this molecule. +    - **Contributor:​** The author, title, volume/​issue,​ pages, etc. of the journal article that had the spectrum, or the source of the spectrum. 
-    - Date: The date this spectrum is digitized (should ​appear automatically). +    - **CASNO:** The unique CAS (Chemical Abstracts Service) registry number assigned to this molecule. 
-    - Digitizer: The user who digizited ​this spectrum (should appear automatically). +    - **Date:** The date this spectrum is digitized (will appear automatically). 
-  - Saving as a .msp file +    - **Digitizer:** The user who digitized ​this spectrum (should appear automatically). 
-    - Click on the Save button. +  - **Saving as a .msp file** 
-    - Find the folder ​in which you want to save the text file. Type the name you want the text file to be saved as. You can choose to add .msp to the end of the filename, but you do not have to. The .msp extension will be added automatically. +    - Put the Mouse pointer ​on the **Save** button ​and click the left Mouse button. This opens a **File Save** dialog box
-    - Click on the Save button in the file chooser ​box. +    - Find the folder ​to which the .msp file is to be saved (Usually the default folder for the //NIST MS Search Program//, C:​\NIST17\MSSearch\). Type the name the .msp file is to be saved as. The .msp extension will be added automatically. 
-    - If you select ​pre-existing ​file, you have the option of overwriting ​the file or appending the current list with its identification information onto the old file. +    - Put the Mouse pointer ​on the **Save** button in the **File Save** dialog ​box and click the left Mouse button
-    - .msp is the default format of the data entered into NIST'​s ​Mass Spectral ​DatabasePlease inquire for details.+    - If a preexisting ​file is selected, the option of **overwriting** or **appending** the file is offered
 +    - .msp is the default format of the data accessed by the //NIST Mass Spectral ​Search Program// 
 +    - The first line of an .msp file starts with **Name:**. Three lines above this is **Digitizer:​** with the information from that field in the Digitizer Program. The next line contains **Date digitized:​** with the information from that field in the Digitizer Program. This is followed by a blank line. These three lines are ignored when the .msp spectrum is imported into MS Search. There is a blank line between the last of //m/z// value intensity pair of a spectrum and the start of the next spectrum. The first line of the next spectrum will have the header **Digitizer:​**. 
 + 
 +To view the contents of the .msp file, open it with Notepad. 
 +{{ :​chemdata:​digispectra1.png?​nolink |}} 
 + 
 + 
  
 === Using keyboard shortcut keys === === Using keyboard shortcut keys ===
- :!: Note: Shortcut keys can only be used if a textbox is not selected. To deselect, click anywhere on the image or the black space.+ :​!: ​**Note:** Shortcut keys can only be used if a textbox is not selected. To deselect, click anywhere on the image or the black space.
  
   - Shortcuts available at all times   - Shortcuts available at all times
-    * - (Minus sign) - Zoom out +    ​* **-** (Minus sign) - Zoom out 
-    * + (Plus sign) - Zoom in +    ​* **+** (Plus sign) - Zoom in 
-    * 0 - Unzoom +    ​* **0** - Unzoom 
-    *- Spacebar ​- Done+    * **Space-bar** - Done
   - Shortcuts available when zooming   - Shortcuts available when zooming
-    * - (Minus sign) - Zoom out +    ​* **-** (Minus sign) - Zoom out 
-    * + (Plus sign) - Zoom in +    ​* **+** (Plus sign) - Zoom in 
-    * 0 - Unzoom +    ​* **0** - Unzoom 
-    * Spacebar ​- Done+    * **Space-bar** ​- Done
   - Shortcuts available when calibrating   - Shortcuts available when calibrating
-    * O - Reset to zoom +    ​* **O** - Reset to zoom 
-    * S - Set X +    ​* **S** - Set X 
-    * A - Add (the Enter key can also be used) +    ​* **A** - Add (the Enter key can also be used) 
-    * W - Highlight Real X textbox +    ​* **W** - Highlight Real X textbox 
-    * Control, ​Shift - Select multiple calibration points +    * **Ctrl** & **Shift** - Select multiple calibration points 
-    * D - Delete selected calibration points +    ​* **D** - Delete selected calibration points 
-    * F - Set Y0 +    ​* **F** - Set Y0 
-    * G - Highlight Real Y0 textbox +    ​* **G** - Highlight Real Y0 textbox 
-    * R - Set Y1 +    ​* **R** - Set Y1 
-    * T - Highlight Real Y1 textbox +    ​* **T** - Highlight Real Y1 textbox 
-    * Z - Left +    ​* **Z** - Left 
-    * C - Right +    ​* **C** - Right 
-    * X - Threshold +    ​* **X** - Threshold 
-    * Spacebar ​- Set Points+    * **Space-bar** ​- Set Points
   - Shortcuts available when manipulating points   - Shortcuts available when manipulating points
-    * O - Reset to zoom +    ​* **O** - Reset to zoom 
-    * P - Reset to calibration +    ​* **P** - Reset to calibration 
-    * Page Up - Select previous point on list +    ​* **Page Up** - Select previous point on list 
-    * Page Down - Select next point on list +    ​* **Page Down** - Select next point on list 
-    * Control, ​Shift - Select multiple data points +    * **Ctrl** & **Shift** - Select multiple data points 
-    * Insert - Add +    ​* **Insert** - Add 
-    * Delete - Delete +    ​* **Delete** - Delete 
-    * Arrow Keys - Move a data point+    * **Left**, **Right**, **Up** and **Down** Arrows ​- Move a data point
  
 === Possible errors === === Possible errors ===
-1. Invalid calibration input +//Spectrum Digitizer Program// will warn about error with pop-up window similar to this:
-You did not enter an integer for one of the calibration inputs (Image/Real X, Y0, Y1). No decimals, letters, other characters, etc. are allowed. +
 {{:​chemdata:​error1.jpg?​nolink|}} {{:​chemdata:​error1.jpg?​nolink|}}
  
-2. Boundaries out of bounds+Description of possible errors is following. 
 + 
 +1. **Invalid calibration input.** \\ 
 +An integer for one of the calibration inputs (Image/Real X, Y0, Y1) was not entered. No decimals, letters, other characters, etc. are allowed. 
 + 
 +2. **Boundaries out of bounds.** \\
 One of the boundary lines is out of bounds. One of the following is happening: One of the boundary lines is out of bounds. One of the following is happening:
   * The left bound is farther left than the left side of the image.   * The left bound is farther left than the left side of the image.
Line 138: Line 180:
   * The threshold line is below the image.   * The threshold line is below the image.
   * The threshold line is above the image.   * The threshold line is above the image.
-{{:​chemdata:​error2.jpg?​nolink|}} 
- 
-3. At least two X values required 
-You can enter in as many X calibration values as you want, but you need to enter in at least two uniqe ones. 
- 
-{{:​chemdata:​error3.jpg?​nolink|}} 
  
-4Calibration points repeated +3**At least two X values required.** \\ 
-You cannot have any repeated ​calibration ​points. You must enter in at least two unique ​calibration values for X.+As many X calibration ​values as wanted can be entered, but there needs to be at least two unique ​ones.
  
-{{:​chemdata:​error4.jpg?​nolink|}}+4. **Calibration points repeated.** \\ 
 +There cannot be repeated calibration points. At least two unique calibration values for X must be entered.
  
-5. Please remove duplicate+5. **Please remove duplicate.** \\
 The final list of x, y values that is save is not allowed to have pairs that share the same X value. Delete or change the duplicate pairs at the X value shown. ​ The final list of x, y values that is save is not allowed to have pairs that share the same X value. Delete or change the duplicate pairs at the X value shown. ​
  
-{{:​chemdata:​error5.jpg?​nolink|}} 
  
chemdata/digitizer.txt · Last modified: 2017/08/17 10:00 (external edit)