pmagpy-cli 4.2.120__tar.gz → 4.2.124__tar.gz

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pmagpy-cli
-Version: 4.2.120
+Version: 4.2.124
 Summary: Analysis tools for paleo/rock magnetic data
 Home-page: https://github.com/PmagPy/PmagPy
 Author: PmagPy team
@@ -166,6 +166,6 @@ This code and the PmagPy cookbook (http://earthref.org/PmagPy/cookbook) are comp
 
 
 
-This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/ltauxe/PmagPy/blob/master/license.txt) for details.
+This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/PmagPy/PmagPy/blob/master/license.txt) for details.
 
 

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/README.md

@@ -86,4 +86,4 @@ This code and the PmagPy cookbook (http://earthref.org/PmagPy/cookbook) are comp
 
 ## Licensing
 
-This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/ltauxe/PmagPy/blob/master/license.txt) for details.
+This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/PmagPy/PmagPy/blob/master/license.txt) for details.

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/pmagpy_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pmagpy-cli
-Version: 4.2.120
+Version: 4.2.124
 Summary: Analysis tools for paleo/rock magnetic data
 Home-page: https://github.com/PmagPy/PmagPy
 Author: PmagPy team
@@ -166,6 +166,6 @@ This code and the PmagPy cookbook (http://earthref.org/PmagPy/cookbook) are comp
 
 
 
-This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/ltauxe/PmagPy/blob/master/license.txt) for details.
+This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/PmagPy/PmagPy/blob/master/license.txt) for details.
 
 

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/programs/atrm_magic.py

@@ -26,8 +26,7 @@ def main():
         -h prints help message and quits
         -f FILE: specify input file, default is atrm_measurements.txt
         -fsp FILE: specimen input file, default is specimens.txt (optional)
-        -Fsp FILE: specify output file, default is specimens.txt (MagIC 3 only)
-        -DM DATA_MODEL: specify MagIC 2 or MagIC 3, default is 3
+        -Fsp FILE: specify output file, default is specimens.txt (optional)
 
     INPUT
         Input for the present program is a TRM acquisition data with an optional baseline.
@@ -58,14 +57,13 @@ def main():
 
     dir_path = pmag.get_named_arg("-WD", ".")
     input_dir_path = pmag.get_named_arg("-ID", "")
-    meas_file = pmag.get_named_arg("-f", "measurements.txt")
-    data_model_num = int(pmag.get_named_arg("-DM", 3))
+    meas_file = pmag.get_named_arg("-f", "atrm_measurements.txt")
     spec_outfile = pmag.get_named_arg("-Fsp", "specimens.txt")
     spec_infile = pmag.get_named_arg("-fsp", "specimens.txt")
 
 
     ipmag.atrm_magic(meas_file, dir_path, input_dir_path,
-                     spec_infile, spec_outfile, data_model_num)
+                     spec_infile, spec_outfile)
 
 
 

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/programs/conversion_scripts/agm_magic.py

@@ -26,6 +26,20 @@ OPTIONS
     -Flo LOCFILE, specify locations.txt file; default is SPEC_locations.txt
     -old : infile is in old format
 
+    NOTES:
+     Sample naming convention:
+    [1] XXXXY: where XXXX is an arbitrary length site designation and Y
+        is the single character sample designation.  e.g., TG001a is the
+        first sample from site TG001.    [default]
+    [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
+    [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
+    [4-Z] XXXX[YYY]:  YYY is sample designation with Z characters from site XXX
+    [5] site name = sample name
+    [6] site name entered in sitename column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
+    [7-Z] [XXX]YYY:  XXX is site designation with Z characters from samples  XXXYYY
+    NB: all others you will have to either customize your
+        self or e-mail ltauxe@ucsd.edu for help.
+
 OUTPUT
     MagIC format files: measurements, specimens, sample, site
 """

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/programs/conversion_scripts/pmd_magic.py

@@ -22,7 +22,8 @@ OPTIONS
     -spc NUM : specify number of characters to designate a  specimen, default = 1
     -loc LOCNAME : specify location/study name
     -A: don't average replicate measurements
-    -dmg TYPE: set default demag type ('t' for thermal, 'af' for AF demag
+    -dmg TYPE: set default demag type ('t' for thermal, 'af' for AF demag) if not 
+               specified in pmd file
     -ncn NCON: specify naming convention
     Sample naming convention:
         [1] XXXXY: where XXXX is an arbitrary length site designation and Y

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/programs/conversion_scripts/run_multi_samples.py

@@ -12,7 +12,7 @@ def main():
         squidm_magic.py program using the command found in files named "commandSample_Name"
         placed in the top file directory. Then it combines the MagIC files into one MagIC 
         text file for uploading. One should run the program in the directory that has the 
-        command files and the sample directories. This program may be for other file formats in the future.
+        command files and the sample directories. This program may be used for other file formats in the future.
 
         The top directory should have the sample directories and the command files. For example:
 
@@ -30,7 +30,7 @@ def main():
                                                                150107_h18.sam (CIT sample list)
                                                      images --> F1_115C_Z_150107_h18_map1.pdf (human viewable image)
                            
-        Run the program in the directory with the commands and sample directories (in the BorlinaEtAl2020 in this example).
+        Run the program in the directory with the commands and sample directories (in BorlinaEtAl2020 for this example).
 
 
     SYNTAX

{pmagpy-cli-4.2.120 → pmagpy-cli-4.2.124}/programs/conversion_scripts/squidm_magic.py

@@ -36,10 +36,17 @@ def main():
         image files that will be uploaded to MagIC along with the data. .jpg, .png,
         .gif, .pdf, etc. type files.
 
-        The .fits file format is: moment in emu, declination, inclination, height, residuals
-        An example of the text in a .fits file:
+        The .fits file format for the "Lima and Weiss 2016" model (use the quoted text as the model name) 
+        is: moment in emu, declination, inclination, height, residuals.
+        An example:
         1.51e-10,54.36,220.92,0.000429,0.4214
 
+        The .fits file format for the "Lima et al. 2023" model (use the quoted text as the model name) 
+        is: moment in emu, declination, inclination, height in meters, residuals, regularization parameter 
+        value (lreg), model order (order), height of the model upward continuation height in meters(upcont). 
+        An example:
+        3.21e-09,-49.92,144.79,0.0020135,0.482282,5,9,0.0002
+
         Example file directory tree:
         ZirconRun1 -- (file hierarchy) 
         ZirconRun2 -- data -- run2N_140C_100k.bz
@@ -63,6 +70,8 @@ def main():
 
         -meas_name_num: set the starting number for the measurement name. Default:1
 
+        -con_id: MagIC contribution id for the dataset
+
         -location: specify location/study name
 
         -location_type: specify location_type 
@@ -126,15 +135,12 @@ def main():
                            Exact instrument name prefered, not type. 
                            (":" between multiple entries)
     
-        -model_height_name: name from the MagIC "Derived Values" controtrolled vocabulary for the model used
-                            to calculate the model height.
-                            Should correspond to the model_residuals_name
+        -model_name: name from the MagIC "Derived Values" controtrolled vocabulary for the model used
+                            to calculate the model parameters (eg. height, residuals, regulariztion parameter,
+                            model order, upward continuation). 
 
-        -model_residuals_name: name from the MagIC "Derived Values" controtrolled vocabulary for the model used
-                            to calculate the model residuals.
-                            Should correspond to the model_height_name
 
-        -model_doi: doi reference for the model used to calculate the model height, and residuals
+        -model_doi: doi reference for the model used to calculate the model height, residuals, lreg, etc.
 
         -A: don't average replicant measurements 
 
@@ -167,8 +173,15 @@ def main():
         [7-Z] [XXX]YYY:  XXX is site designation with Z characters from samples  XXXYYY
         NB: all others you will have to either customize your self or e-mail webmaster@earthref.org for help.
 
-      Example command for the example data file. Data from Weiss et al., 2018 (doi:10.1130/G39938.1):
-    squidm_magic.py -location "Jack Hills" -location_type "Outcrop" -geologic_classes "Metamorphic" -lithologies "Metaconglomerate" -geologic_types "Single Crystal" -lat "-26" -lon 117 -age_low 0.8 -age_high 2.6 -age_unit Ga -citations "10.1130/G39938.1" -site "Erawandoo Hill" -loc_method_codes "GM-UPB" -site_method_codes "GM-UPB" -samp_method_codes "SC-SQUIDM" -spec_method_codes "SC-SQUIDM" -geologic_types "Single Crystal" -sample RSES-57 -ncn 5 -instrument_codes "MIT SQUID microscope" -model_height_name "SQUID Microscopy Model Height Lima And Weiss 2016" -model_residuals_name "SQUID Microscopy Residuals Lima And Weiss 2016" -model_doi "10.1002/2016GC006487" -labfield 50.0 -phi 0.0 -theta 90 -A
+      Example command for MagIC data file (earthref.org/MagIC/17000).  Data from Weiss et al., 2018 
+        (doi:10.1130/G39938.1). Uses the Lima and Weiss, 2016 modeling technique. 
+
+      squidm_magic.py -location "Jack Hills" -location_type "Outcrop" -geologic_classes "Metamorphic" -lithologies "Metaconglomerate" -geologic_types "Single Crystal" -lat "-26" -lon 117 -age_low 0.8 -age_high 2.6 -age_unit Ga -citations "10.1130/G39938.1" -site "Erawandoo Hill" -loc_method_codes "GM-UPB" -site_method_codes "GM-UPB" -samp_method_codes "SC-SQUIDM" -spec_method_codes "SC-SQUIDM" -geologic_types "Single Crystal" -sample RSES-57 -ncn 5 -instrument_codes "MIT SQUID microscope" -model_name "Lima And Weiss 2016" -model_doi "10.1002/2016GC006487" -labfield 50.0 -phi 0.0 -theta 90 -A
+      
+      Example command for MagIC data file ().  Data from (doi:). 
+      Uses the Lima et al. 2023 modeling technique. 
+
+squidm_magic.py -con_id 20187 -location "Crevice Cave" -location_type "Region" -geologic_classes "Sedimentary" -lithologies "Carbonate" -geologic_types "Sediment Layer" -lat "37.8" -lon "-89.8" -age_low 24 -age_high 28 -age_unit ka -citations "10.1130/G39938.1" -site "Cave" -loc_method_codes "GM-UTH" -site_method_codes "GM-UTH" -samp_method_codes "SC-SQUIDM" -spec_method_codes "SC-SQUIDM" -sample CC -ncn 5 -instrument_codes "MIT SQUID microscope" -model_name "Lima et al. 2024" -model_doi "10.1029/2022GC010724" -labfield 200.0 -phi 0.0 -theta 0 -A -multi_samples
     """
 
     if '-h' in sys.argv: # check if help is needed
@@ -181,47 +194,54 @@ def main():
     else:
         meas_name_num=1
 
+    if '-con_id' in sys.argv:
+        ind=sys.argv.index('-con_id')
+        con_id=sys.argv[ind+1]
+    else:
+        print("The MagIC contribution id must be set with the -con_id flag")
+        sys.exit()
+   
     if '-location' in sys.argv:
         ind=sys.argv.index('-location')
         location=sys.argv[ind+1]
     else:
         print("The location/study name must be set with the -location flag")
-        exit()
+        sys.exit()
    
     if '-location_type' in sys.argv:
         ind=sys.argv.index('-location_type')
         location_type=sys.argv[ind+1]
     else:
         print("The location_type name must be set with the -location_type flag")
-        exit()
+        sys.exit()
    
     if '-geologic_classes' in sys.argv:
         ind=sys.argv.index('-geologic_classes')
         geologic_classes=sys.argv[ind+1]
     else:
         print("The geologic classes must be set with the -geologic_classes flag")
-        exit()
+        sys.exit()
    
     if '-lithologies' in sys.argv:
         ind=sys.argv.index('-lithologies')
         lithologies=sys.argv[ind+1]
     else:
         print("The litothologies must be set with the -lithologies flag")
-        exit()
+        sys.exit()
    
     if '-lat' in sys.argv:
         ind=sys.argv.index('-lat')
         lat=sys.argv[ind+1]
     else:
         print("The latitude must be set with the -lat flag")
-        exit()
+        sys.exit()
    
     if '-lon' in sys.argv:
         ind=sys.argv.index('-lon')
         lon=sys.argv[ind+1]
     else:
         print("The longitude must be set with the -lon flag")
-        exit()
+        sys.exit()
    
     if '-age' in sys.argv:
         ind=sys.argv.index('-age')
@@ -251,8 +271,8 @@ def main():
         ind=sys.argv.index('-age_unit')
         age_unit=sys.argv[ind+1]
     else:
-        print("The age unit must be set with the -ageunit flag")
-        exit()
+        print("The age unit must be set with the -age_unit flag")
+        sys.exit()
 
     if '-citations' in sys.argv:
         ind=sys.argv.index('-citations')
@@ -271,21 +291,21 @@ def main():
         site_method_codes=sys.argv[ind+1]
     else:
         print("method code(s) for the site must be set with the -site_method_code flag")
-        exit()
+        sys.exit()
    
     if '-samp_method_codes' in sys.argv:
         ind=sys.argv.index('-samp_method_codes')
         samp_method_codes=sys.argv[ind+1]
     else:
         print("method code(s) for the sample must be set with the -samp_method_code flag")
-        exit()
+        sys.exit()
    
     if '-spec_method_codes' in sys.argv:
         ind=sys.argv.index('-spec_method_codes')
         spec_method_codes=sys.argv[ind+1]
     else:
         print("method code(s) for the specimen must be set with the -specimen_method_code flag")
-        exit()
+        sys.exit()
    
     if '-meas_method_codes' in sys.argv:
         ind=sys.argv.index('-meas_method_codes')
@@ -301,47 +321,40 @@ def main():
     else:
         instrument_codes=""
         
-    if '-model_height_name' in sys.argv:
-        ind=sys.argv.index('-model_height_name')
-        model_height_name=sys.argv[ind+1]
+    if '-model_name' in sys.argv:
+        ind=sys.argv.index('-model_name')
+        model_name=sys.argv[ind+1]
     else:
-        print("The model height name must be set with the -model_height_name flag")
-        exit()
-   
-    if '-model_residuals_name' in sys.argv:
-        ind=sys.argv.index('-model_residuals_name')
-        model_residuals_name=sys.argv[ind+1]
-    else:
-        print("The model residuals name must be set with the -model_residuals_name flag")
-        exit()
-   
+        print("The model name must be set with the -model_name flag")
+        sys.exit()
+        
     if '-model_doi' in sys.argv:
         ind=sys.argv.index('-model_doi')
         model_doi=sys.argv[ind+1]
     else:
         print("The model doi must be set with the -model_doi flag")
-        exit()
+        sys.exit()
    
     if '-site' in sys.argv:
         ind=sys.argv.index('-site')
         site=sys.argv[ind+1]
     else:
         print("The site name must be set with the -site flag")
-        exit()
+        sys.exit()
    
     if '-geologic_types' in sys.argv:
         ind=sys.argv.index('-geologic_types')
         geologic_types=sys.argv[ind+1]
     else:
         print("The  geologic types must be set with the -geologic_types flag")
-        exit()
+        sys.exit()
    
     if '-sample' in sys.argv:
         ind=sys.argv.index('-sample')
         sample=sys.argv[ind+1]
     else:
         print("The site name must be set with the -sample flag")
-        exit()
+        sys.exit()
 
     if '-oe' in sys.argv:
         oe=' -oe '
@@ -395,7 +408,7 @@ def main():
         ncn=sys.argv[ind+1]
     else:
         print("Setting the sample name convention with the -ncn flag is required")
-        exit()
+        sys.exit()
 
 
 #   Run cit_magic.py on all slides to process the psudo-Thellier data
@@ -404,6 +417,8 @@ def main():
 
     print("start")
 
+    print("con_id=",con_id)
+
     os.system("rm locations.txt sites.txt samples.txt specimens.txt measurements.txt")
     os.system("rm *.txt ") # for debugging
     os.system("rm -r images")
@@ -477,7 +492,15 @@ def main():
         
         # create MagIC files from cit files
         os.chdir(dir+'/demag')     
-        command='cit_magic.py -ncn ' + ncn + ' -f ' + dir + '.sam -loc "' + location + '" -sn "' + site + '" -sampname "' + sample + '" -dc ' + labfield + ' '  + phi + ' ' + theta + ' ' + average
+        # find .sam file name
+        sam_file=""
+        sam_list=os.listdir()
+        for file in sam_list:
+            if ".sam" in file:
+                sam_file=file
+                break
+                
+        command='cit_magic.py -ncn ' + ncn + ' -f ' + sam_file + ' -loc "' + location + '" -sn "' + site + '" -sampname "' + sample + '" -dc ' + labfield + ' '  + phi + ' ' + theta + ' ' + average
         if spec_method_codes != "":
             command+=' -mcd ' + spec_method_codes
         print(command)
@@ -503,15 +526,15 @@ def main():
 
         # Create the large MagIC measurement files for the raw QDM data scans
         os.chdir('../data')     
-        os.system('rm measurements*.txt')
-        meas_num,meas_name_num=convert_squid_data(specimen,citations,meas_num,meas_method_codes,meas_name_num,model_height_name,model_residuals_name,model_doi)
-        os.system('mv measurements*.txt ../../') 
+        os.system('rm magic_measurements*.txt')
+        meas_num,meas_name_num=convert_squid_data(con_id,specimen,citations,meas_num,meas_method_codes,meas_name_num,model_name,model_doi)
+        os.system('mv magic_measurements*.txt ../../') 
 
         os.chdir('../../')
 
 #   move all the measurement files to one folder
     os.system("mkdir measurements")
-    os.system("mv measurements[0-9]*.txt measurements")
+    os.system("mv magic_measurements_"+con_id+"\.[0-9]*.txt measurements")
 
 #   Combine the images tables and put the images in one folder
     image_files=""
@@ -567,7 +590,7 @@ def main():
     os.system("combine_magic.py -F specimens.txt -f " + spec_files)
     os.system("combine_magic.py -F measurements.txt -f " + meas_files)
 
-    os.system("upload_magic.py")
+    os.system("upload_magic.py -all")
 
 #   Remove MagIC files
     for dir in slide_dir_list:
@@ -587,7 +610,7 @@ def main():
     print("end")   
     return()
 
-def convert_squid_data(specimen,citations,meas_num,meas_method_codes,meas_name_num,model_height_name,model_residuals_name,model_doi):
+def convert_squid_data(con_id,specimen,citations,meas_num,meas_method_codes,meas_name_num,model_name,model_doi):
 #   Take the SQUID magnetometer files and make a MagIC measurement file. This data will not be uploaded 
 #   in the contribution MagIC data file due is large size, but will be available for download. 
 #   These have to be uploaded by hand for now.
@@ -697,12 +720,18 @@ def convert_squid_data(specimen,citations,meas_num,meas_method_codes,meas_name_n
         line=f.readline()
         line_split=line.split(",")
         # fit file values are moment (emu), inc, dec, height and residuals
+        # or
+        # moment (emu), inc, dec, height, residuals, lreg, order, upcont
         height=line_split[3]
         residuals=line_split[4]
         residuals=residuals.strip()
+        if len(line_split) > 5:
+            lreg=line_split[5]
+            order=line_split[6]
+            upcont=str.strip(line_split[7])
 
 # open the measurement file for writing and put the compressed headers in
-        mf=open('measurements'+str(meas_num)+'.txt','w')
+        mf=open('magic_measurements_'+con_id+'.'+str(meas_num)+'.txt','w')
         mf.write("tab\tmeasurements\n")
         mf.write('* experiment\t'+experiment_name+'\n')
         mf.write('* specimen\t'+specimen+'\n')
@@ -711,7 +740,13 @@ def convert_squid_data(specimen,citations,meas_num,meas_method_codes,meas_name_n
         mf.write('* method_codes\t'+meas_method_codes+'\n')
         mf.write('* citations\t'+citations+'\n')
         mf.write('* description\t'+comment+'\n')
-        mf.write('* derived_value\t'+model_height_name+','+height+','+model_doi+';'+model_residuals_name+','+residuals+','+model_doi+'\n')
+        mf.write('* derived_value\t'+"SQUID Microscopy Model Height "+model_name+','+height+','+model_doi+';'+
+                 'SQUID Microscopy Model Residuals '+model_name+','+residuals+','+model_doi+';')
+        if model_name == "Lima et al. 2023":
+            mf.write('SQUID Microscopy Model Regularization Parameter '+model_name+','+lreg+','+model_doi+';'+
+                     'SQUID Microscopy Model Order '+model_name+','+order+','+model_doi+';'+
+                     'SQUID Microscopy Model Upward Continuation Height '+model_name+','+upcont+','+model_doi)
+        mf.write('\n')
 
         mf.write('measurement\tmagn_z\tmeas_pos_x\tmeas_pos_y\n')
         print('meas_num=', meas_num)