MagIC  |  Help Contents  |  Full Text  |  Feedback    

MagIC Help Library

First  |  Previous  |  Next  |  Last    

4.3.3  Data Reduction Menu

When you pull down the "Data reduction" menu, you will see these options:

The zeq_redo file contains instructions for how to interpret measurement data for a standard demagnetization experiment. The first column is the specimen name, the second is the directional estimation method codes (DE-BFL for best-fit lines, DE-BFP for best-fit planes and DE-FM for Fisher means). The third column is the beginning demagnetization step for the calculation and the fourth is the end. Please note that these must be in the units required by the MagIC database, so are tesla for AF demagnetization and kelvin for thermal demagnetization. All magnetometer data are translated into these units. To convert mT to tesla, multiply by 10-3, Oe to tesla, multiply by 10-4 and from degrees C to kelvin, add 273. The fifth column is an optional component name. If none are supplied, the first interpretation for a given specimen is named "A" and the second is named "B", etc.

The thellier_redo file contains instructions for how to interpret measurement data for a double heating paleointensity experiment. The first column is the specimen name, the second is the beginning demagnetization step for the calculation and the third is the ending demagnetization step. Units must be in oC. To convert from degrees C to kelvin, add 273.

When you select the "PmagPy redo" option, the MagIC.py GUI copies the redo file into your project MagIC directory and executes the commands zeq_magic_redo.py or thellier_magic_redo.py, depending on what you imported. This program hunts through measurement data (in the magic_measurements.txt file) for data matching each specimen name, collects the data between the two end points specified in the redo file and does the desired calculation. The specimen calculations are written to a pmag_specimen formatted file called either zeq_specimens.txt or thellier_specimens.txt within your project MagIC directory. These interpretations will be read in when you try the Demagnetization data or Thellier-type experiments as described below.

The DIR (ASCII) format is a file format used by the PaleoMac program developed at IPG by J.-P. Cogne. Here is an example of the ASCII version of these files:

The meanings of the various columns is described on the PaleoMac website. This option copies the selected file to the MagIC project directory and generates a call to the program DIR_magic.py. This translates the file into a zeq_redo formatted file (see above) called DIR_redo. It then called zeq_magic_redo.py to make a file called zeq_specimens_DIR with the MagIC formatted specimen directions in it. Note: this will overwrite any "DIR_redo" file already imported, so put ALL your interpretations into a single .DIR file! To assemble different specimen direction files together, choose "Assemble Specimens" as described below.

The LSQ format imports the interpretions stored in the .LSQ files output by the Craig Jones program PaleoMag and described on this website. Here is an example of the data format:

To use this option efficiently concatenate all the .LSQ files from a particular study into a single .LSQ file. You can do this by typing the command: cat *.LSQ >myLSQ on your command line if you are in the directory in which all the .LSQ files are located. Alternatively, you can import each .LSQ file individually. On choosing this option, you are asked to specify the file name to be imported and then whether or not you want to overwrite your previous specimen interpreation files. If you are importing all the interprations in a single .LSQ file (recommended), you should select the "overwrite" radio button. If you don't, you will generate a file called zeq_specimens_LSQ.txt which you can select when assembling your results.

The LSQ option first copies the .LSQ file into your MagIC project directory, then calls the program LSQ_redo.py. This program does two things: it creates a zeq_redo formatted file (see above) and it modifies the magic_measurements.txt file to mark the sample_flag to 'b' for bad for the excluded data points as indicated in the .LSQ file. Then the MagIC GUI generates pmag_specimen formatted file. You then should select "assemble specimens" and check your interpretations using the "Demagnetization Data" plotting option described below.

customize selection criteria

  • Customize Criteria: PmagPy programs allow you to select data for further calculation (sample or site means, inclusion in final results table, etc.) based on quantitative criteria. The criteria are recorded in the pmag_criteria table in the MagIC database. These can be customized for your particular needs using the "Customize Criteria" option. Selecting this makes a call to the PmagPy program customize_criteria.py.
  • The first window allows you to specify what sort of criteria file you want to create:

    You can either use the default criteria or change them to suit your own needs. You can modify a criteria file you created before or apply no selection criteria. For changing default of existing criteria, you will then be asked to customize a series of criteria. The first is for choosing directional data for specimens:

    Next you can select criteria for intensity data at the specimen level:

    Next you can select criteria for directional data at the sample level (based on averages of multiple specimens:

    On the next page, you can customize the same parameters but for the site level:

    Here you customize your criteria for site level directions:

    Demagnetization data

    The left-hand plot is an equal area projection of the demagnetization data. The title is the specimen name and the coordinate system of the plot. Solid symbols are lower hemisphere projections. The directions of lines fit through the data are shown as blue diamonds. Green dotted lines (not shown) are the lower hemisphere projections of a best-fit plane while cyan is on the upper hemisphere. The red line is the X direction (NRM) of the middle plot.

    The middle plot is a vector-end point diagram. The magnetization vectors are broken down into X,Y,Z components (depending on the coordinate system). The default for this plot is to rotate the X direction such that it is parallel to the NRM direction. Solid symbols are the horizontal projection (X,Y) and open symbols are the X,Z pairs - the plane containing X,Z is shown as the solid red line in the left-hand plot. The open diamonds are the end points for the calculations of any components from prior interpretations. Green lines are best-fit lines. The numbers are the demagnetization steps shown in the terminal window. The title is the specimen name, the coordinate system and the NRM intensity (in the units of the magic_measurements table, so are SI.

    the right-hand plot is the behavior of the intensity during demagnetization. Numbers are the demagnetization steps listed in the terminal window. The green line is the magnetization lost at each step.

    You control the program through the terminal window:

    The program writes out the specimen name and its number out of the total, then looks for previous interpretations. If it finds one, it draws the direction or plane on the plot windows and prints out summary data: the specimen name, the number of steps included in the calculation, the MAD or alpha_95 (depending on calculation type), the start and end demagnetization steps, the declination and inclination of the directed line or pole to the best-fit plane, the calculation type (best-fit line, plane or fisher mean or DE-BFL, DE-BFP, DE-FM respectively) and the component name.).

    Then, the program prints out the data for the specimen. Each measurement is annotated "g" for good or "b" for bad depending on the measurement_flag in the data file and numbered. The demagnetization level is given in mT or oC. The strength is in SI units and the declination and inclination are in the coordinate system specified in the titles of the plot figures.

    The program can be controlled by entering letters on the command line. Hitting the return (or enter) key will step to the next specimen.

  • Typing an 'a' [followed by the return key] saves the plot in the default file format (.svg) [Note, you can save the plots in other formats by clicking on the save button and specifying the desired format as .svg, .jpg, .png, etc.]
  • 'b' will generate a prompt asking for the step numbers of the start and end steps for calculation and calculation type. If there is already an interpretation for this specimen, the program will automatically increment the component name.
  • If you want to delete the existing interpretations, type 'd' on the command line.
  • To step backwards through the specimens, type 'p'.
  • To select a particular specimen, type 's'.
  • To change the horizontal axis, type 'h'
  • and the coordinate system, type 'c'.
  • If there is a data point that is clearly a 'bad' measurement, select 'e'. This will allow you to choose a particular measurement step. The program will mark its measurement_flag as 'b' and plot the point as an open diamond. The data point is not erased - just marked as bad and excluded from calculations. Be very careful with this option! You will be asked if you want to change the magic_measurements file to preserve these designations.
  • When you have stepped through all the specimens, or typed 'q' to quit, the program quits and control is returned to the GUI window. If it seems stuck, click on the python icon on your dock (Macs only) and the GUI will respond again (usually!).

    Thellier-type experiments

  • Thellier-type experiments : This option allows you to plot double heating paleointensity experimental data. First the MagIC.py GUI looks for prior interpretations (the thellier_specimens.txt file created in previous sessions or by importing prior interpretations). Then, it constructs the command line argument calling the program thellier_magic.py. This program steps through the measurement data (in magic_measurements.txt) specimen by specimen, making at least four plots:
  • The left-hand plot (labeled Figure 3) is an Arai plot of the double heating experiment. The title is the specimen name and NRM intensity of the specimen. Solid symbols are zero-field first then in-field heating pairs (ZI) data and open symbols are in-field first, then zero field pairs (IZ). The temperature pairs are numbered for reference with the data list in the terminal window. The blue squares are "pTRM-tail checks" and the triangles are "pTRM" checks. If you have selected end points for inclusions in the slope calculation, these will be marked by diamonds and the green line is the best-fit line through the data points. The field intensity will be noted (B: ) in microtesla and a grade assigned according to the selection criteria. To change these, use the "customize criteria" option described above. The line labeled "VDS" is the vector difference sum of the zero field data.

    The middle plot is a vector-end point diagram. The magnetization vectors are broken down into X,Y,Z components (these are in specimen coordinates here with the X direction rotated such that it is parallel to the NRM direction. Solid symbols are the horizontal projection (X,Y) and open symbols are the X,Z pairs. The open diamonds are the end points for the calculations of any components from prior interpretations. Green lines are best-fit lines. The numbers are the demagnetization steps shown in the terminal window. The title is the specimen name and the NRM intensity (in the units of the magic_measurements table, so are SI.

    The right-hand plot is the behavior of the intensity during demagnetization and remagnetization. Numbers are the demagnetization steps listed in the terminal window.

    The fourth plot is an equal area projection of the zero field steps from the ZI steps (circles) and the IZ steps (squares) as well as the direction of the pTRM acquired at each step (triangles). This should of course be parallel to the lab field direction and deviation therefrom is a hint that the specimen is anisotropic. Only the steps included in the slope calculation are plotted.

    You control the program through the terminal window:

    The program writes out the specimen name and its number out of the total, then looks for previous interpretations. If it finds one, it draws the interpretations on the plot windows and prints out summary data: specimen name, lower and upper temperature steps (Tmin, Tmax), the number of steps used in the calculation, N, the lab field assumed, lab_field, the ancient field estimate (no corrections) B_anc and a host of other statistics: b q f(coe) Fvds beta MAD Dang Drats Nptrm Grade R MD% sigma Z Gmax which are described in the Essentials of Paleomagnetism online text book. The program also looks for TRM acquisition data and anisotropy data. If it finds it, it will print out the "corrected data" as well, including the corrected pTRM acquisition steps - a proper anisotropy correction will bring the best-fit line through these into alignment with the laboratory applied field direction. If the program finds TRM aquisition data, there will be a fifth plot, showing these data as well and the correction inferred therefrom.

    The program thellier_magic.py can be controlled by entering letters on the command line. Hitting the return (or enter) key will step to the next specimen.

  • Typing an 'a' [followed by the return key] saves the plot in the default file format (.svg) [Note, you can save the plots in other formats by clicking on the save button and specifying the desired format as .svg, .jpg, .png, etc.]
  • 'b' will generate a prompt asking for the step numbers of the start and end steps for calculation.
  • If you want to delete the existing interpretations, type 'd' on the command line.
  • To step backwards through the specimens, type 'p'.
  • To select a particular specimen, type 's'.
  • To change the horizontal axis, type 'h'
  • When you have stepped through all the specimens, or typed 'q' to quit, the program quits and control is returned to the GUI window. If it seems stuck, click on the python icon on your dock (Macs only) and the GUI will respond again (usually!). When you are done, be sure to select "Assemble specimens."

  • Microvwave experiments:
  • Anisotropy data

  • Anisotropy data:If you have imported your anisotropy data and assembled the measurements, you can plot the anisotropy data with this option. You can plot various types of confidence ellipses (Hext and several styles of bootstrap ellipses) and choose to plot either all the data in the rmag_anisotropy.txt file (created when you assemble your measurements) or site by site:
  • For a complete discussion of confidence ellipses see Chapter 13 in the Web Edition of the book Essentials of Paleomagnetism, by Tauxe et al. (2009). In this example, we elected to plot both the Hext ellipses and the bootstrap ellipses. To suppress the latter, check the box labelled '-B' in the options window. For now, we get this plot:

    In Figure 1 (to the right), we have plotted the eigenvectors from site tr24. Red squares are the eigenvectors associated with the maximum eigenvalues for each specimen. Blue triangles are the intermediate and black circles are the minima. All plots are lower hemisphere equal area plots. Figure 2 (middle) shows the two forms of confidence ellipses. The rounder, larger ellipses are the Hext ellipses. Green lines are plotted on the upper hemisphere. Figure 3 (left) shows cumulative distributions of bootstrapped eigenvalues and their 95% confidence bounds (vertical lines). Because each eigenvalue is distinct from the others (the confidence bounds do not overlap), this site has a triaxial fabric. These plots can be saved in a variety of formats by clicking on the disk icons to on the figure tool bars by choosing the appropriate name (e.g., myfig.png saves the file in the png format) or by typing an "a" on the command line in the terminal window. [P] [P] To control the program, type in commands on the command line in your terminal window:

    You can change coordinate systems (if you have imported orientation information along with your anisotropy files) by typing a "c", ellipses style, by typing an "e". You can also plot a direction (a lineation observed in the outcrop) or a great circle (the plane of a dike) for comparison. You can also step forward to the next site or back to the previous one. The summary statistics for each ellipse calculation are also printed out in the terminal window. The tau_i are the eigenvalues and the V_i are the eigenvectors. The D's and I's are declinations and inclinations and the zeta and eta are the semi-axes of the major and minor ellipses respectively. These summary statistics calculated by aniso_magic.py are also stored in the file rmag_results.txt in the project MagIC directory.

    Hysteresis Data

  • Hysteresis data:This option allows you to plot and interpret simple hysteresis experiments. If you have imported your hysteresis data using the PmagPy software (for example, through the GUI as described in the section on importing hysteresis data, you can use this option to make calls to the program hysteresis_magic.py, which reads in the magic_measurements.txt file in your MagIC project directory. The program looks for all the data with the method code "LP-HYS" and assembles the data by specimen, calculates the high field slope (Xhf) by averaging both "ends" of the loop. It subtracts this off, closes the loop and calculates the coercivity (Bc), saturation magnetization (Ms) and saturation remanence (Mr). The red line in the left-hand plot below is the "raw" data and the blue line is the corrected data. In the middle plot, we show the difference between the ascending and descending loops in the left-hand plot (the Delta M). This is calculated by first taking a spline of the data and resampling at equal values of B. The point at which Delta M reaches 50% of its initial value is an estimate of the coercivity of remanence (Bcr). The right hand plot is the deriviative of the middle plot and represents the switching field distribution. For more on what these parameters mean and on hysteresis data in general see Tauxe et al., 2009.
  • If you also imported data from "back-field" IRM experiments, you will also see a plot like this:

    The point at which the remanence is reduced to zero is another estimate for coercivity of remanence. The various hysteresis parameters that are calculated by hysteresis_magic.py are stored in the datafiles rmag_hysteresis and rmag_remanence in the project MagIC directory.

  • Hysteresis parameters:After you have looked at the hysteresis data with hysteresis_magic.py (see option labelled "Hysteresis data" above), you can plot various hysteresis parameters against one another using this option. The left hand plot plots the ratios of Mr/Ms versus Bcr/Bc. These are frequently interpreted in terms of magnetic domain state (see Chapter 5 of Tauxe et al. 2009 for a more complete discussion.) The middle plot is is the Mr/Ms ratio (squareness) plotted versus the coercivity (Bc) and the right hand plot is squareness versus coercivity of remanence (Bcr). If you have imported back-field data, you will have two estimates for Bcr, one from the Delta M curve (plotted in blue squares) and one from the back field data (red dots).
  • Plot IRM acquisition data: Under construction.
  • Assemble specimen data

  • Assemble specimens: After you have examined the relevant plots for your data set and interpreted the data to your satisfaction, you must select this option. This will recalculate all the specimen directions in desired coordinates, it will do anisotropy corrections and non-linear TRM corrections on thellier data if you have imported the necessary data and assemble all the specimen interpretation files generated during plotting into a single pmag_specimens.txt file. Details of each record are reflected in the magic_method_codes.
  • Check sample orientations: If you are going to calculate site mean directions for your data, you might find it useful to check your sample orientations. This option calls the program site_edit_magic.py. This first asks you if you want to re-consider all the previously rejected sample orientations, or just check the remaining ones:
  • Then, the program steps through the data by site, plotting all the directions in geographic coordinates.

    If you find a site with a suspicious sample, you can select 'e' and type in that specimen name on the command line. The program calculates possible specimen directions assuming several common types of errors in the field. Triangle: wrong arrow for drill direction, e.g., out of the outcrop instead of in. Delta: someone read the wrong end of compass. Small circle: wrong mark on sample [cyan upper hemisphere]. Paleomagnetitsts often mark the sample orientation with a brass rod, then extract the sample with a "shoe horn" of some sort. It is possible that when marking the sample, a stray mark was used. In this case, the "real" specimen direction will lie along the dotted line. If any of these possibilities brings the specimen direction into the group of other directions, you can mark this sample orientation as "bad" with a note as to why you have excluded it. The data do not disappear from the data base, but your rationale for excluding a particular result is explained in the er_samples table. The result can be excluded from site means, etc.

    When you are done with editing sample orientations, be sure to select "Assemble specimens" again. This will recalculate the specimen tables, excluding the "bad" orientation data from geographic and tilt corrected records.

    Assemble result data

  • Assemble results: When you are ready to calculate site mean directions and intensities, convert them to VGPs and V[A]DMs, etc., select this option which calls the program specimens_results_magic.py. All records in the MagIC data base (except synthetic samples) must have some age bounds associated with them. Therefore, MagIC.py asks you for these age bounds and attaches them to any record that does not have its own date in an er_ages table in the project MagIC directory.
  • Then you are asked which (of the possibly many) specimen files you wish to work on. The default is the pmag_specimens.txt file generated by the "Assemble specimens" option. If for example, you only want to work on a particular one, select "customize choice". Usually you will want the default specimen file.

    The next window allows you to control which data are selected and how they are treated. To use the selection criteria chosen by you in the "Customize Criteria" section, check the box marked '-exc'. -aD and -aI do the averages by sample, then by site instead of treating all specimens as individuals at the site level. -sam puts sample level VGPs and/or V[A]DMs on the results table. -p plots directions by site so you can have a last check on what is going into the er_sites and pmag_results tables. Virtual Axial Dipole moments (VADM) require an estimate of paleolatitude. This could be the present latitude (-lat option) or a reconstructed paleolatitude (-fla). For the latter, you will have to enter the site name and your best estimate for paleolatitude in a separate file (model_lat.txt). This file should be copied into the project MagIC directory. This latitude will be saved as the model_lat on the results table. If you want to calculate paleolatitudes for a given site, use the "Expected directions/paleolatitudes" option under the Utilities menu. By skipping directions or intensities if you have no relevant data, you can speed up processing time.

    If you have multiple coordinate systems available (e.g., specimen, geographic, tilt corrected), you can choose which coordinate systems you want to include on the pmag_results table:

    The specimens_results_magic.py program processes the data, averaging by sample (if desired) and by site. It combines best-fit lines and planes at the site level using the technique of McFadden and McElhinny (1988) and calculates VGPs and V[A]DMs as approprite and creates the files pmag_samples.txt, pmag_sites.txt and pmag_results.txt in the project MagIC directory.

  • Extract results to table: reformats the information in the various files to create three files: Directions.txt, Intensities.txt and SiteNFO.txt. These are tab delimited files that can be put directly in your manuscripts for publication.
  • Prepare Upload txt file: This option calls the program upload_magic.py. This hunts through the project MagIC directory and assembles all the relevant datafiles into a file called upload_dos.txt. This file can be imported into the MagIC console, where additional information, such as the location information, age data, and citation information can be added. The data file can then be prepared for uploading into the database.