Make ready for v1.3.4

Author: ronnyerrmann

HiFLEx_UserManual.pdf

@@ -15,6 +15,7 @@ If you publish data using the barycentric correction, please cite (https://githu
 * Extra logging information for wavelength solution and drift of the wavelength solution
 * Improved measurement of the offset between emission line spectra and the wavelength solution
 * Bugfixing and improvement of parallelisation; optional excludition of steps to speed up
+* GUI to add/modify the automatically found orders
 
 ## Install instruction
 
@@ -68,7 +69,7 @@ Create a new folder and copy the `conf.txt` file from your HiFLEx installation p
   * Define what files should be used for what calibration.
   * Define what files to extract (and in which RVs will be measured).
   * Please note that you can use already reduced images. In this case the reduction steps as defined in `conf.txt` should be empty for the file type (e.g. dark or real flats) to avoid a second application of the correction.
-- Run the scrip `hiflex.py`
+- Run the script `hiflex.py`
 - Afterwards: check the output in the `logfile`, the images in the logging path, or in results in the extracted files.
 
 More information can be found in the [manual](https://github.com/ronnyerrmann/HiFLEx/blob/master/HiFLEx_UserManual.pdf).

HiFLEx_UserManual.tex

@@ -6,7 +6,7 @@
 #   create_badpx_mask.py
 #   file_assignment.py
 #   hiflex.py
-#   remove_orders.py
+#   emove_add_modify_orders.py
 
 ## Format of the parameters:
 #---------------------------
@@ -68,7 +68,7 @@ bin_search_apertures    = 20,2
   # bin_adjust_apertures: Adjust the center of the apertures in a less binned image. Description as for bin_search_apertures. The second value should be 1 to reach best precission
   #                 format: list of two integers
 bin_adjust_apertures    = 3,1
-  # What is the brightest pixel of the faintest order (after binning). The higher this number the quicker, but fainter orders might not be traced
+  # What is the brightest pixel of the faintest order (after binning, which is done calculating the average). The higher this number the quicker, but fainter orders might not be traced
 traces_searchlimit_brightness = 2000
 traces_searchlimit_brightness = 200
   # polynom_order_apertures: Order of the polynomial to define the form of the traces along the CCD

README.md

@@ -9395,8 +9395,17 @@ def getcoords_from_file(obnames, mjd, filen='coords.txt', warn_notfound=True, ig
                         except:
                             logger('Warn: Problem with the declination of entry {1} in the reference coordinates file {0}.'.format(filen,cos))
                             break
-                    PMRA = float(cos[3])    # mas/yr
-                    PMDEC = float(cos[4])   # mas/yr
+                    prob_list = ['', '--']
+                    if cos[3] not in prob_list:
+                        try:
+                            PMRA = float(cos[3])    # mas/yr
+                        except:
+                            logger('Warn: Problem with the proper motion in RA of entry {1} in the reference coordinates file {0}.'.format(filen,cos))
+                    if cos[4] not in prob_list:
+                        try:
+                            PMDEC = float(cos[4])   # mas/yr
+                        except:
+                            logger('Warn: Problem with the proper motion in DEC of entry {1} in the reference coordinates file {0}.'.format(filen,cos))
                     try:
                         epoch = float(cos[8])
                     except:

conf.txt

@@ -59,13 +59,12 @@
                             logger('Warn: Cannot create directory {0}'.format(params[entry]))
 
     # Save the new file and restart the reduction
-    logger('Info: New file with the traces was created. All data depending on this will be moved to the folder {0}, the traces will be written and hiflex.py will be run'.format(params['folder_original_traces']))
+    logger('Info: New file with the traces was created. All data depending on this will be moved to the folder {0}, the traces will be written.'.format(params['folder_original_traces']))
     save_fits_width(polyfits, xlows, xhighs, widths, params['master_trace_sci_filename'])
     plot_traces_over_image(im_flat, params['logging_traces_im'].replace('*', 'master_trace1'), polyfits, xlows, xhighs, widths)
 
     cmd = 'python {0}/hiflex.py {1}'.format(os.path.dirname(sys.argv[0]), ' '.join(sys.argv[1:]) )
-    print('\n')
-    logger('Info: Finished removing traces. Now, please run the pipeline again:\n{0}'.format(cmd))
+    logger('Info: Finished modifying traces. Now, please run the pipeline again:\n{0}'.format(cmd))
 
     log_params(params)