Echelle improvements

maven_iuvs/__init__.py

@@ -16,6 +16,9 @@
 from . import constants
 from . import integration
 from . import file_classes
+from . import binning
+from . import echelle
+
 
 try:
     from .user_paths import auto_spice_load as _auto_spice_load

maven_iuvs/binning.py

@@ -0,0 +1,133 @@
+import numpy as np
+
+def get_binning_scheme(hdul):
+    """
+    Gets the binning scheme for a given FITS HDU.
+
+    Parameters
+    ----------
+    hdul : astropy FITS HDUList object
+           HDU list for a given observation
+
+    Returns
+    -------
+    Dicionaries explaining the binning scheme:
+    if nonlinear, returns the bin table, along with the number of spatial and spectral bins.
+    if linear, returns the first spatial and spectral bin edges, the widths, and the number of bins.
+
+    """
+    if hdul['PRIMARY'].header['NAXIS'] == 1:
+        nspa = 0
+        nspe = 0
+    else:
+        nspe = hdul['PRIMARY'].header['NAXIS1']
+        nspa = hdul['PRIMARY'].header['NAXIS2']  
+
+    bintbl = hdul['PRIMARY'].header['BIN_TBL']
+    if 'NON LINEAR' in bintbl:
+        return {'bintbl':bintbl,'nspa':nspa, 'nspe':nspe}
+
+    spebinwidth = hdul['PRIMARY'].header['SPE_SIZE']
+    spabinwidth = hdul['PRIMARY'].header['SPA_SIZE']
+
+    spepix0 = hdul['PRIMARY'].header['SPE_OFS']
+    spapix0 = hdul['PRIMARY'].header['SPA_OFS']
+
+    return {'spapix0':spapix0, 'spabinwidth':spabinwidth, 'nspa':nspa,
+            'spepix0':spepix0, 'spebinwidth':spebinwidth, 'nspe':nspe,}
+
+
+def pix_to_bin(hdul, pix0, pix1, spa_or_spe, return_npix=True):
+    """
+    Converts pixels to bins on the detector in either the spatial or 
+    spectral dimenison. 
+
+    Parameters
+    ----------
+    hdul : astropy FITS HDUList object
+           HDU list for a given observation
+    pix0 : int
+           Lowest pixel number in the given dimension to include
+    pix1 : int
+           Highest pixel number in the given dimension to include
+    spa_or_spe : string
+                 indicates whether this function will convert spatial or 
+                 spectral pixels to bins
+    return_npix : boolean
+                  whether to return the total number of pixels calculated
+
+    Returns
+    -------
+    binlo : int
+            Index of lowest bin encompassed by [pix0, pix1] in pixels
+
+    binhi : int
+            Index of highest bin encompassed by [pix0, pix1] in pixels
+    npix : int
+           number of total pixels in the enclosed bins
+
+    """
+    binpixlo = hdul['Binning'].data[spa_or_spe+'PIXLO'][0]
+    binpixhi = hdul['Binning'].data[spa_or_spe+'PIXHI'][0]
+    binpixwidth = binpixhi+1 - binpixlo
+    nbins = len(binpixlo)
+    binlo = np.searchsorted(binpixlo, pix0+0.01) - 1
+    binlo = 0 if binlo < 0 else binlo
+    binhi = np.searchsorted(binpixhi, pix1-0.01) + 1
+    binhi = nbins if binhi > nbins else binhi
+
+    if return_npix:
+        npix = np.sum(binpixwidth[binlo:binhi])
+        return binlo, binhi, npix
+
+    return binlo, binhi
+
+
+def get_pix_range(myfits, which="spatial"):
+    """
+    Given a fits observation, gets the range of pixels
+    for either the spatial or spectral dimension.
+
+    Parameters
+    ----------
+    myfits : IUVSFITS or astropy FITS HDUList object
+             IUVS FITS file in question
+    which: string
+           "spatial" or "spectral"
+
+    Returns
+    ----------
+    Array of pixel values for bin edges.
+    """
+    pixlo = myfits['Binning'].data[f'{which[:3]}pixlo'][0]
+    pixhi = myfits['Binning'].data[f'{which[:3]}pixhi'][0]
+
+    if not (set((pixhi[:-1]+1)-pixlo[1:]) == {0}):
+        raise ValueError("Error in bin table")
+
+    pixrange = np.concatenate([[pixlo[0]], pixhi+1])
+
+    return pixrange
+
+
+def get_npix_per_bin(myfits):
+    """Calculates total pixels per bin.
+
+    Parameters
+    ----------
+    myfits: astropy FITS HDUList object
+            IUVS observation data file
+
+    Returns
+    ----------
+    npixperbin : int
+                 number of pixels per bin
+    """
+    spapixrange = get_pix_range(myfits, which="spatial")
+    spepixrange = get_pix_range(myfits, which="spectral")
+
+    spepixwidth = spepixrange[1:]-spepixrange[:-1]
+    spapixwidth = spapixrange[1:]-spapixrange[:-1]
+
+    npixperbin = np.outer(spapixwidth, spepixwidth)
+    return npixperbin

maven_iuvs/download.py

@@ -75,7 +75,6 @@ def setup_user_paths():
 
     Notes
     -------
-
     This is an interactive routine called once, generally the first
     time the user calls sync_data.
 
@@ -131,11 +130,13 @@ def setup_user_paths():
     user_paths_file.write("iuvs_vm_username = \""+vm_username+"\"\n")
     user_paths_file.write("auto_spice_load = "+auto_spice_load+"\n")
     user_paths_file.close()
-    # now scripts can import the relevant directories from user_paths
 
+    # now scripts can import the relevant directories from user_paths
 
+
 def get_default_data_directory(level='l1b'):
-    """Returns default l1b_dir defined in user_paths.py, creating the
+    """
+    Returns default l1b_dir defined in user_paths.py, creating the
     file if needed.
 
     Parameters
@@ -170,7 +171,6 @@ def get_default_data_directory(level='l1b'):
 
     return local_dir
 
-
 def call_rsync(remote_path,
                local_path,
                ssh_password,
@@ -219,9 +219,9 @@ def call_rsync(remote_path,
         progress_flag = '--progress'
 
     # Add some code to handle a case where spaces in the local folder path will cause rsync to fail silently
-    if " " in local_dir:
-        local_dir = local_dir.replace(" ", "\ ")
-        
+    if " " in local_path:
+        local_path = local_path.replace(" ", "\ ")
+
     rsync_command = " ".join(['rsync -trvzL',
                               progress_flag,
                               extra_flags,
@@ -236,6 +236,7 @@ def call_rsync(remote_path,
     cpl = child.compile_pattern_list([pexpect.EOF,
                                       '.* password: ',
                                       '[0-9]+%'])
+
     while True:
         i = child.expect_list(cpl, timeout=None)
         if i == 0:  # end of file
@@ -431,8 +432,8 @@ def sync_data(spice=True, level='l1b',
     Returns
     -------
     None.
-
     """
+
     # setup search pattern
     pattern = get_filename_glob_string(**filename_kwargs)
 
@@ -482,10 +483,11 @@ def sync_data(spice=True, level='l1b',
         else:
             raise ValueError('local_dir must be l1a or l1b')
 
-    # Check to be sure that the vm is in the known_hosts file.
+     # Check to be sure that the vm is in the known_hosts file.
     is_vm_found = subprocess.run(["ssh-keygen", "-H", "-F", vm], capture_output=True)
     if (is_vm_found.returncode == 1) or ("found" not in is_vm_found.stdout.decode('utf-8')):
-        raise Exception(f"{vm} is not in the list of known_hosts. Please manually connect via ssh; upon first connection, it will be added automatically to ~./.ssh/known_hosts.")
+        raise Exception(f"{vm} is not in the list of known_hosts. Please manually connect"
+                         " via ssh; upon first connection, it will be added automatically to ~./.ssh/known_hosts.")
 
     # try to sync the files, if it fails, user probably isn't on the VPN
     try:
@@ -505,6 +507,7 @@ def sync_data(spice=True, level='l1b',
         # sync level 1B data
         if level is not None:
             # get the file names of all the relevant files
+            print(f"Running sync on {datetime.datetime.utcnow().strftime('%a %d %b %Y, %I:%M%p')}")
             print('Fetching names of production and stage'
                   ' files from the VM...')
             prod_filenames = get_vm_file_list(vm,
@@ -780,7 +783,8 @@ def get_integrated_reports_dir():
 
 
 def sync_integrated_reports(sdc_username, sdc_password, check_old=False):
-    """Sync Integrated Reports data from MAVEN Ops page. Syncs all new
+    """
+    Sync Integrated Reports data from MAVEN Ops page. Syncs all new
     files and all files from last 180 days by default.
 
     Parameters
@@ -796,7 +800,6 @@ def sync_integrated_reports(sdc_username, sdc_password, check_old=False):
     Returns
     -------
     none
-
     """
 
     print("syncing Integrated Reports... ")
@@ -899,4 +902,4 @@ def sync_sdc(check_old=False):
     password = getpass('password for '+username+' on MAVEN Team SDC: ')
 
     sync_euvm_l2b(username, password)
-    sync_integrated_reports(username, password, check_old=check_old)
+    sync_integrated_reports(username, password, check_old=check_old)