Some short videos of the screen action will help you understand how the pitch information is displayed. A graph of the tune unfolds against a background of horizontal lines representing each of the 12 notes of the scale. They are labeled on the left margin, with the rather more easily grasped Hindustani notation. The seven shuddh swaras, Sa, Re, Ga, Ma, Pa, Dha, & Ni are labeled, and are drawn with solid color lines. The komal re, ga, dha, ni and tivra ma lie in-between, and are drawn with dotted lines.

Their twelve separate colors help you keep your place on the graph easily. (Imagine trying to distinguish your location amongst several dozen gray lines). Note that pairs of notes have related colors - bright green for Re, dark green for komal re; bright red for Ma, dark red for tivra ma; and so on.

The way the Carnatic notes lie against this representation is shown below.

  

Here's a short passage on bansuri to illustrate:

    The portion of the screen below the splitter bar is a fine-tuning graph - a magnified view of the pitch of each individual note. That is, while the time axis remains the same in both the upper and lower graphs, in the lower graph the vertical direction is stretched quite a lot so that you can see the pitch in much greater detail.

The horizontal center line, with the label 0, of the graph represents "in tune" with the nearest note being sung, according to the scale and pitch selected. The other labels at the left [2] indicate that each dashed line represents a pitch differential of 10 cents. The color of the trace of the graph serves to label which note of the scale is being measured, and it changes as the tune moves from note to note, matching the color of the nearest line on the upper chart. The boxes [3] show how the same pitch space (vertical) is portrayed in both the lower and upper graph; the space in the upper graph, where a note is closest to Pa than to ma or dha, is stretched vertically and fills the height of the lower graph. The first box shows the tambura, aligned with the center. Then the flute plays a Pa, whose color is brown. The boxes in the upper and in the lower graphs cover the same pitch space - the lower graph magnifies the space around Pa, which in the upper graph is only a few pixels high. When the next note dha begins, the lower graph switches to its color, dark red-purple. Then comes Ni, pale blue, which in this case happens to be quite a bit sharper than the note given by theorists. [A thin black line through the trace gives the average value - of course in order to represent an average it cannot start until a certain number of pixels after a new note begins]. We continue with Sa (quite a bit sharp) in dark blue, bright green Re, greenish-yellow ga, Re again, Sa [way better in tune], and Ni.  Much greater pitch detail can be seen than in the upper graph of the overall tune. The lower graph is where you can examine the precision of the intonation of a recording, and with a microphone, your own playing or singing. We see that the first Sa is quite a bit sharp, the second one quite precisely in tune with the tambura. Ni is sharp both times - probably this is the way the player has grown up with that swara. It is quite useful to observe how consistent different performers are, and of course to strive for greater consistency yourself.
    The final note on this clip wanders sort of midway between Dha and dha so it changes back and forth between two colors. 

    Again, the key to understanding the lower graph is that the color of the trace signifies the note being graphed.  The lower graph moves between representing first one note, then another.  The color-labeling allows a seamless graph where time moves across at an even pace; note names or other symbols won’t work because there can’t be an interruption in the smooth horizontal flow of the graph, which corresponds to the passage of time.
 
    Indian music naturally involves lots of gliding between notes, fast gamakas and so forth; all these quick ornaments, and movements in between notes, can be seen in the trace in the upper graph. And they generally move so fast that the lower graph becomes just a jumble of color - so you just ignore it for those passages. But whenever the performer alights on a note, the lower graph will give quite precise detail as to the subtlety of the shruti involved. We can see that the graph is very closely aligned with the tambura. The tambura trace seems rather vague; it may be because its sound is not so closely recorded, but it may just be that, as a very straight sound it makes a very narrow, non-wiggly line and is a bit hidden behind the black center line. And you will usually find that even a fixed sound like the tambura or harmonium will wander a few cents - the harmonium because of subtle changes in the bellows pressure. The same is true of an open violin string - different bow pressure will change the pitch a small but easily seen amount.
 

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    Now you should try actually observing the graph for yourself, through a microphone. You can start the tuning process from Options | Tuning Graph. 

    You may need to manipulate the Recording controls to feed the music to the software. Most of the utility of the program takes place simply by watching the graph; most of the things you need to learn involve how to set parameters appropriate to the moment, but once launched your sessions really involve simply interacting with the pitch information, perhaps using the feedback it provides to sharpen your hearing and your sense of shruti. 

    You will have to set some parameters. To monitor a performance you clearly need to align the graph to the singer or instrument of the moment, and to achieve this you set Options | Pitch of Sa & Range.

Depending on your program version, and the screen width, you might see a slightly different arrangement of this dialog, either this:


or this:

    Note this last form of the dialog box is made quite wide so it can be as shallow as possible; that allows a bit less of the tuning screen to be hidden.
    For Indian music you usually want to accommodate the graph to an existing sound; for instance, you are pretty much stuck with the pitch of a harmonium, or a flute.  This process is shown in the video below, where the shruti box is set near E. This would fit got instance a male vocalist with a slightly higher than normal range, which is often C#, the starting point in the video. Note that the line in the Upper Graph begins as a komal ga, relative to the C#. We adjust the slider Nearest Piano Note to Sa [1] three times to the right, bringing the reference Sa to Re, komal re, and finally it appears as the dark blue representing Sa. Now it is close but it is not yet right on the reference line; it is sharp more than 50 cents. So we raise the pitch to meet that - by moving the slider giving the pitch (Hz) for the corresponding western "A" [2] until the blue trace sits on the exact center of the lower graph. In this case the pitch line was above the center, so we raised our reference pitch; had it been below the center, we would have lowered the reference to meet the line.
[It is helpful to know that moving the slider for the pitch of A by one "page" value changes it by 5 Hz, which is very close to 20 cents at 440 Hz. So we use that motion twice, to come close, before pressing an end arrow or the left/right arrow key for fine adjustment by 0.1 Hz].

[Alternatively, you might directly select the note you like to sing on, and set your shruti box pitch to lie on the center line.]

    The Indian vocal - female or male entry supplied under the Instruments menu item is just a starting point, sort of average. Some vocalists sing several notes higher, some lower. Adjust your Sa as we have shown. Also, you may perhaps sing notes lower than M or higher than P and need to adjust the Lowest [3] and Highest note [4] entries accordingly. [The Concert Pitch labels just give the western note names for the bottom and top notes of the graph].
    Keeping the Relative Range Constant [5] should always be the selection for Indian music. It will allow you to move from one Sa to another while the relative range, from M to P will always remain the same. If you have the program version limited to raga performance, that control has been removed to make life simpler for you.

    In certain modes of practice it is useful to have the graph trace stop when input ceases; similar to a voice-activated recording mode. For instance you may wish to sing or play a short phrase without looking at the graph, then check to see if your sense of intonation corresponds with what the graph drew. To switch between continuous trace or input-activated start and stop, check View | Trace Continuous [or input dependent].

    You won't want to have to adjust these parameters of Pitch of Sa & Range every time and so for that we turn to the Instruments menu, where you can save and later retrieve different settings for your work with Tuning Meister.