Thu Feb 22 16:30:45 MST 2018

MANIFEST

@@ -1,23 +1,21 @@
 # file GENERATED by distutils, do NOT edit
-LICENSE
-README.md
 setup.cfg
 setup.py
-data/newbex/bs/mosaic_100.tiff
-data/newbex/bs/mosaic_200.tiff
-data/newbex/bs/mosaic_400.tiff
-data/newbex/ref/newbex_bed.cpg
-data/newbex/ref/newbex_bed.dbf
-data/newbex/ref/newbex_bed.prj
-data/newbex/ref/newbex_bed.qpj
-data/newbex/ref/newbex_bed.shp
-data/newbex/ref/newbex_bed.shx
 prism/__init__.py
 prism/common_funcs.py
 prism/crf_funcs.py
 prism/eval_funcs.py
 prism/gmm_funcs.py
 prism/gui_funcs.py
+prism/newbex_bed.cpg
+prism/newbex_bed.dbf
+prism/newbex_bed.prj
+prism/newbex_bed.qpj
+prism/newbex_bed.shp
+prism/newbex_bed.shx
+prism/newbex_mosaic_100.tiff
+prism/newbex_mosaic_200.tiff
+prism/newbex_mosaic_400.tiff
 prism/plot_funcs.py
 prism/prism_logo_blk_sm.png
 prism/read_funcs.py

README.md

@@ -5,5 +5,10 @@ A Python framework for Probabilistic Acoustic Sediment Mapping. See project webs
 
 
 ### Contributing & Credits
-Primary Developer:    Daniel Buscombe, Northern Arizona University, Flagstaff, AZ 86011, [email protected]
+Software Developer: Dr. Daniel Buscombe, Northern Arizona University, Flagstaff, AZ 86011, [email protected]
 
+Example backscatter data (.tiff files) originate from data collected by R2Sonic and distributed for use as part of the R2Sonic 2017 Multispectral Backscatter competition.
+
+Bed observation data from Patricia Bay are digitized from data presented in: B.~Biffard. Seabed remote sensing by single-beam echosounder: models, methods and applications. Doctoral dissertation, University of Victoria, Canada, 2011.
+
+Bed observation data from Portsmouth (NEWBEX) are digitized from data presented in: T.~Weber, L.~and Ward. Observations of backscatter from sand and gravel seafloors between 170 and 250 kHz. Journal of the Acoustical Society of America, vol.~138, no.~4, pp.~2169 - 2180, 2015.

prism/__init__.py

@@ -1,12 +1,30 @@
 # encoding: utf-8
+#    ____  ____  ___ ____  __  __     
+#   |  _ \|  _ \|_ _/ ___||  \/  |  _ 
+#   | |_) | |_) || |\___ \| |\/| | (_)
+#   |  __/|  _ < | | ___) | |  | |  _ 
+#   |_|   |_| \_\___|____/|_|  |_| (_)
+#                                     
+#   ___                 _      _                  __                   __      
+#    | _  _ ||_  _ \/ _|__ ._ |_).__ |_  _.|_ o|o(__|_o _  /\  _ _    (__|_o _ 
+#    |(_)(_)||_)(_)/\  |(_)|  |  |(_)|_)(_||_)|||__)|_|(_ /--\(_(_)|_|__)|_|(_ 
+#                                                                              
+#    __                                          
+#   (_  _  _|o._ _  _ .__|_ |\/| _.._ ._ o._  _  
+#   __)(/_(_||| | |(/_| ||_ |  |(_||_)|_)|| |(_| 
+#                                  |  |       _| 
+#
+#   |b|y| |D|a|n|i|e|l| |B|u|s|c|o|m|b|e|
+#   +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+#   |d|a|n|i|e|l|.|b|u|s|c|o|m|b|e|@|n|a|u|.|e|d|u|
 
-__version__ = '0.0.15'
+__version__ = '0.0.19'
 
 #-----------------------------------------------------------------------------
 # Imports
 #-----------------------------------------------------------------------------
 __all__ = ['common_funcs', 'crf_funcs', 'gmm_funcs', 'read_funcs',
-           'write_funcs', 'eval_funcs', 'gui_funcs'] #, 'test']
+           'write_funcs', 'eval_funcs', 'gui_funcs', 'test']
 
 from . import common_funcs
 from . import crf_funcs

prism/eval_funcs.py

@@ -69,7 +69,8 @@ def plot_confmatGMM(y_pred, Lc, bed, prefix):
    This function ...
    """
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    y = y_pred.copy()
    del y_pred
@@ -114,7 +115,8 @@ def plot_confmatCRF(y_pred, Lc, bed, prefix):
    This function ...
    """
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    y = y_pred.copy()
    del y_pred

prism/gui_funcs.py

@@ -49,6 +49,7 @@
 from PIL import Image, ImageTk
 
 # prism functions
+import prism
 from prism.common_funcs import *
 from prism.crf_funcs import *
 from prism.gmm_funcs import *
@@ -144,8 +145,8 @@ def gui():
 	image_panel.grid(column = 0, row = 2)
 	image_panel.configure(background='black')
 
-	#show_image = ImageTk.PhotoImage(Image.open(prism.__path__[0]+os.sep+"prism_logo_blk.png"))
-	show_image = ImageTk.PhotoImage(Image.open("prism_logo_blk_sm.png"))
+	show_image = ImageTk.PhotoImage(Image.open(prism.__path__[0]+os.sep+"prism_logo_blk_sm.png"))
+	#show_image = ImageTk.PhotoImage(Image.open("prism_logo_blk_sm.png"))
 	# show the panel
 	image_panel.create_image(0, 0, anchor=Tkinter.NW, image=show_image) 
 

prism/newbex_bed.cpg

@@ -0,0 +1 @@
+UTF-8

prism/newbex_bed.prj

@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]

prism/newbex_bed.qpj

@@ -0,0 +1 @@
+GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]]

prism/plot_funcs.py

@@ -40,7 +40,8 @@ def plot_bs_maps(img, bed, bs, cmap, prefix):
    latmin = bs[0]['latmin']  
    latmax = bs[0]['latmax']
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    cmap = colors.ListedColormap(cmap)
 
@@ -261,7 +262,8 @@ def plot_dists_per_sed(Lc, img, bed, cmap, prefix):
    This function ...
    """
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    cmap = colors.ListedColormap(cmap)
 
@@ -363,7 +365,8 @@ def plot_gmm(mask, y_pred, y_prob, bs, bed, cmap, prefix):
    latmin = bs[0]['latmin']  
    latmax = bs[0]['latmax']
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    #----------------------------------------------------------------
 
@@ -465,7 +468,8 @@ def plot_gmm_image(mask, y_pred, y_prob, bs, bed, cmap, prefix):
 
    cmap = colors.ListedColormap(cmap)
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    #----------------------------------------------------------------
    X = bed['Xlon']
@@ -584,7 +588,8 @@ def plot_crf(mask, y_pred, y_prob, bs, bed, cmap, prefix):
    y_prob[mask==1] = np.nan   
    y_pred[mask==1] = np.nan
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    cmap = colors.ListedColormap(cmap)
 
@@ -690,7 +695,8 @@ def plot_crf_image(mask, y_pred, y_prob, bs, bed, cmap, prefix):
    y_prob[mask==1] = np.nan   
    y_pred[mask==1] = np.nan
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    cmap = colors.ListedColormap(cmap)
 
@@ -819,7 +825,8 @@ def plot_gmm_crf(mask, y_pred_gmm, y_prob_gmm, y_pred_crf, y_prob_crf, bs, bed,
    latmin = bs[0]['latmin']  
    latmax = bs[0]['latmax']
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    #----------------------------------------------------------------
 
@@ -999,7 +1006,8 @@ def plot_gmm_crf_images(mask, y_pred_gmm, y_prob_gmm, y_pred_crf, y_prob_crf, bs
    y_prob_crf[mask==1] = np.nan   
    y_pred_crf[mask==1] = np.nan
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    cmap = colors.ListedColormap(cmap)
 

prism/test.py

@@ -29,6 +29,7 @@
 import os
 
 # prism functions
+import prism
 from prism.common_funcs import *
 from prism.crf_funcs import *
 from prism.gmm_funcs import *
@@ -37,10 +38,34 @@
 from prism.eval_funcs import *
 from prism.plot_funcs import *
 
+import os
+import shutil
+import errno
+
+def dircopy(src, dest):
+    try:
+        shutil.copytree(src, dest)
+    except OSError as e:
+        # If the error was caused because the source wasn't a directory
+        if e.errno == errno.ENOTDIR:
+            shutil.copy(src, dest)
+        else:
+            print('Directory not copied. Error: %s' % e)
+
+__all__ = [
+    'dotest',
+    ]
+
 ##-------------------------------------------------------------
 
 def dotest():
 
+
+   # copy files over to somewhere read/writeable
+   dircopy(prism.__path__[0], os.path.expanduser("~")+os.sep+'prism_test')
+
+   # general settings   
+
    ##GMM parameters
    covariance = 'full'
    tol = 1e-2
@@ -57,10 +82,16 @@ def dotest():
    prob_thres = 0.1
    chambolle = 0.0
    test_size = 0.5
-   bs100 = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'bs'+os.sep+'mosaic_100.tiff'
-   bs200 = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'bs'+os.sep+'mosaic_200.tiff'
-   bs400 = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'bs'+os.sep+'mosaic_400.tiff'
-   refs_file = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'ref'+os.sep+'newbex_bed.shp'
+
+   bs100 = os.path.normpath(os.path.join(os.path.expanduser("~"),'prism_test','newbex_mosaic_100.tiff'))
+   bs200 = os.path.normpath(os.path.join(os.path.expanduser("~"),'prism_test','newbex_mosaic_200.tiff'))
+   bs400 = os.path.normpath(os.path.join(os.path.expanduser("~"),'prism_test','newbex_mosaic_400.tiff'))
+   refs_file = os.path.normpath(os.path.join(os.path.expanduser("~"),'prism_test','newbex_bed.shp'))
+
+   #bs100 = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'bs'+os.sep+'mosaic_100.tiff'
+   #bs200 = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'bs'+os.sep+'mosaic_200.tiff'
+   #bs400 = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'bs'+os.sep+'mosaic_400.tiff'
+   #refs_file = '..'+os.sep+'data'+os.sep+'newbex'+os.sep+'ref'+os.sep+'newbex_bed.shp'
    prefix = 'newbex'
 
    input = [bs100, bs200, bs400]

prism/write_funcs.py

@@ -32,7 +32,8 @@ def export_bed_data(bed, prefix):
    This function ...
    """
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    rows = zip(bed['Xlon'], bed['Ylat'], bed['Cnames'], bed['Ccodes'])
 
@@ -55,6 +56,14 @@ def export_bed_data(bed, prefix):
                 'geometry': mapping(point)
             })
 
+   # create the .prj file
+   prj = open(base+'bed_observations.prj', "w")
+   # call the function and supply the epsg code
+   epsg = 'GEOGCS["WGS84",DATUM["WGS_1984",SPHEROID["WGS84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.01745329251994328,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]]'
+   prj.write(epsg)
+   prj.close()
+
+
 ##-------------------------------------------------------------
 def export_crf_gtiff(mask, y_pred, y_prob, bs, prefix):
    """
@@ -68,7 +77,8 @@ def export_crf_gtiff(mask, y_pred, y_prob, bs, prefix):
    prob[mask==1] = np.nan   
    pred[mask==1] = np.nan
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    proj = osr.SpatialReference()
    proj.ImportFromEPSG(4326) 
@@ -137,7 +147,8 @@ def export_gmm_gtiff(mask, y_pred, y_prob, bs, prefix):
    prob[mask==1] = np.nan   
    pred[mask==1] = np.nan
 
-   base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   #base = '..'+os.sep+'outputs'+os.sep+prefix+'_'
+   base = prefix+'_'
 
    proj = osr.SpatialReference()
    proj.ImportFromEPSG(4326)