Merge branch 'dev_adhoc_to_fits'

Necessary to make PyQubeVis work with new options

PyQubeVis.py

@@ -29,7 +29,8 @@ import astropy.io.fits as fits
 import numpy as np
 import gzip
 #import pywcs
-import ipdb
+#import ipdb
+import argparse
 
 from PyQt5 import QtGui, QtCore, QtWidgets
 from PyQt5.QtWidgets import QApplication, QMainWindow, QTextEdit, QPushButton, QMessageBox
@@ -613,6 +614,108 @@ class MainWindow(QMainWindow, Ui_PyQubeVis):
             print('Problem encountered when saving file')
 
 
+    def openfile_cl(self, fname):
+        '''Open from command line call to PyQubeVis'''
+        #Determination of extension
+        if fname == '':
+            return
+        namesplit = os.path.splitext(fname)
+        ext = namesplit[1].lower()
+        if ext == '.gz':
+            ext = os.path.splitext(namesplit[0])[1] + ext
+
+        #File reading depending on extension
+        if ext == '.fits':
+            hdu = fits.open(fname)
+        elif ext == '.fits.gz':
+            hdu = fits.open(gzip.open(fname))
+        elif ext == '.ad2':
+            dtu = pad.read_ad2(fname)
+            hdu = dtu.tohdu()
+        elif ext == '.ad2.gz':
+            dtu = pad.read_ad2(gzip.open(fname))
+            hdu = dtu.tohdu()
+        elif ext == '.ad3':
+            dtu = pad.read_ad3(fname)
+            hdu = dtu.tohdu()
+        elif ext == '.ad3.gz':
+            dtu = pad.read_ad3(gzip.open(fname))
+            hdu = dtu.tohdu()
+        else:
+            return
+
+        hdr = hdu[0].header
+        data = hdu[0].data
+
+        if self.numim == 0:
+            self.displayScrollAreaWidgetContents.setEnabled(True)
+        #Running path update
+        #(self.path, filen) = os.path.split(fname)
+        (self.path, filen) = os.path.split(fname)
+
+        #Update of data arguments
+        #self.argfiles['fullfilename'].append(fname)
+        #self.colorTableList = QtColorTable()
+        self.argfiles['fullfilename'].append(fname)
+        self.argfiles['filename'].append(filen)
+        self.argfiles['data'].append(np.array(data))
+        self.argfiles['sum'].append(None)
+        self.argfiles['sumhighthr'].append(None)
+        self.argfiles['sumlowthr'].append(None)
+        self.argfiles['issum'].append(0)
+        self.argfiles['profilenumber'].append(1)
+        self.argfiles['header'].append(hdr)
+        if np.size(np.shape(data)) == 1:
+            self.argfiles['sx'].append(np.shape(data)[0])
+            self.argfiles['sy'].append(0)
+            self.argfiles['sz'].append(0)
+            self.argfiles['numcube'].append(0)
+        if np.size(np.shape(data)) == 2:
+            self.argfiles['sx'].append(np.shape(data)[1])
+            self.argfiles['sy'].append(np.shape(data)[0])
+            self.argfiles['sz'].append(0)
+            self.argfiles['numcube'].append(0)
+        if np.size(np.shape(data)) == 3:
+            self.argfiles['sx'].append(np.shape(data)[2])
+            self.argfiles['sy'].append(np.shape(data)[1])
+            self.argfiles['sz'].append(np.shape(data)[0])
+            self.numberofcubes += 1
+            self.argfiles['numcube'].append(self.numberofcubes)
+
+        #A mettre a jour correctement ou enlever?
+        self.argfiles['pixmap'].append(None)
+        self.argfiles['zoompixmap'].append(None)
+        self.argfiles['actionimage'].append(None)
+        self.argfiles['actionprofile'].append(None)
+        self.argfiles['highthr'].append(np.nanmax(data))
+        self.argfiles['lowthr'].append(np.nanmin(data))
+        self.argfiles['ctinvert'].append(False)
+        self.argfiles['ctscale'].append('Lin')
+        self.argfiles['max'].append(np.nanmax(data))
+        self.argfiles['min'].append(np.nanmin(data))
+        self.argfiles['colortable'].append(self.createColorTable(self.defaultColorTable))
+        self.argfiles['zoom'].append(1.)
+        self.argfiles['flipx'].append(False)
+        self.argfiles['flipy'].append(False)
+        self.argfiles['mask'].append(None)
+        self.argfiles['highmask'].append(None)
+        self.argfiles['lowmask'].append(None)
+        value_range = np.nanmax (data) - np.nanmin (data)
+        if value_range == 0:
+            formatval = 0
+        else:
+            formatval = np.ceil(- np.log10(value_range) + 4)
+        self.argfiles['thresholdstep'].append(str(10 ** (-formatval + 3)))
+        if formatval < 0: formatval = 0
+        formatval = '%.' + '%if'%formatval
+        self.argfiles['formatval'].append(formatval)
+
+        self.numim = np.size(self.argfiles['filename'])
+        if np.size(np.shape(data)) == 3:
+            self.numcube = self.numim
+        self.firstDisplay()
+
+
     def openfile(self):
         '''Popup to select the file to open'''
         #Il faudrait empecher de modifier le filtre
@@ -903,12 +1006,18 @@ class MainWindow(QMainWindow, Ui_PyQubeVis):
                           platform.python_version(), PYQT_VERSION_STR, QT_VERSION_STR))
 
 
-def main():
+def main(argv):
     app = QApplication(sys.argv)
+    #parser = argparse.ArgumentParser()
+    #parser.add_argument('filename', action="store", default='', help="name of the file to open")
+    #options = parser.parse_args(app.arguments()[1:])
+    #print(options.filename, len(options.filename))
     frame = MainWindow()
+    for fname in sys.argv[1:]:
+        frame.openfile_cl(fname)
     frame.show()
     sys.exit(app.exec_())
 
 if __name__ == '__main__':
-    main()
+    main(sys.argv[1:])
 

README.md

@@ -17,4 +17,7 @@ To be executable, PyQubeVis.py has to be in the PATH
 
 ## Usage
 
+Files can be opened directly from the command line. The names must be indicated:
+PyQubeVis.py file_1 file_2 ... file_n
 **PyQubeVis** can be used to visualise cubes in the **adhocw** format. It can also be used to manually clean 2D maps. Using *control* or *shift* allows to clean/select regions.
+

pyadhoc.py

@@ -868,7 +868,9 @@ def ad3_to_fits(ad3_file, fits_file=None, overwrite=False, header_from=None):
     if fits_file is None:
         fits_file = ad3_file + '.fits'
 
-    tdu = read_ad3(ad3_file)
+    tdu = read_ad3(ad3_file)  # XXX Could also be with other read_ad3 options...
+    
+    # XXX We might use a function tdu_to_hdu to do the core of this function and just read and write here. Same for other format conversion (ad2_to_fits, fits_to_ad?)
 
     assert tdu.data.ndim == 3
 
@@ -1061,6 +1063,8 @@ def fits_to_adhoc(fits_filename, adhoc_filename, adhoc_trailer=None,
 
 
 def fits_header_to_ad2trailer(header):
+    
+    # Should use a default header first and then update what is important, same for other metadata transformations.
     dt = np.dtype(TRAILER_AD2)
     trailer = np.empty(1, dtype=dt)[0]