move requirements.txt to the root dir (#772)

* mv requirements.txt to root dir for a shorter path + move requirements.txt from ./docs to ./ dir for a shorter path; update path in installations.md and circleci/config.yml + utils.utils1.update_template_file(): handle value2seach inside if check, to avoid unnecessary running * view: add --coastline-lw / --lalo-off / --lalo-fs + view: add 3 new options to customize plotting in geo-coordinates: - coastline-linewidth - lalo-offset - lalo-fontsize + asc_desc2horz_vert: - bugfix on the printout msg during REF_LAT/LON checking - bugfix on the output metadata in one output HDF5 fil + readfile: GDAL related metadata - DATA_TYPE_GDAL2NUMPY/NUMPY2GDAL: add cint16/32 for translation purpose - add ".tiff" to GDAL_FILE_EXTS
insarlab · May 10, 2022 · 7014b0b · 7014b0b
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -38,7 +38,7 @@ jobs:
             export PATH=${CONDA_PREFIX}/bin:${PATH}
             # install dependencies and source code
             source activate root
-            mamba install --verbose --yes gdal">=3" --file ${MINTPY_HOME}/docs/requirements.txt
+            mamba install --verbose --yes gdal">=3" --file ${MINTPY_HOME}/requirements.txt
             python -m pip install ${MINTPY_HOME}
             # test installation
             smallbaselineApp.py -v

diff --git a/docs/installation.md b/docs/installation.md
@@ -22,7 +22,7 @@ Then complete the [post-installation setup](#3-post-installation-setup).
 
 Note: The installation note below is tested on Linux and macOS, and is still experimental on Windows (may has bugs).
 
-MintPy is written in Python 3 and relies on several Python modules, check the [requirements.txt](https://github.com/insarlab/MintPy/blob/main/docs/requirements.txt) file for details. We recommend using [conda](https://docs.conda.io/en/latest/miniconda.html) or [macports](https://www.macports.org/install.php) to install the python environment and the prerequisite packages, because of the convenient management and default [performance setting with numpy/scipy](http://markus-beuckelmann.de/blog/boosting-numpy-blas.html) and [pyresample](https://pyresample.readthedocs.io/en/latest/installation.html#using-pykdtree).
+MintPy is written in Python 3 and relies on several Python modules, check the [requirements.txt](https://github.com/insarlab/MintPy/blob/main/requirements.txt) file for details. We recommend using [conda](https://docs.conda.io/en/latest/miniconda.html) or [macports](https://www.macports.org/install.php) to install the python environment and the prerequisite packages, because of the convenient management and default [performance setting with numpy/scipy](http://markus-beuckelmann.de/blog/boosting-numpy-blas.html) and [pyresample](https://pyresample.readthedocs.io/en/latest/installation.html#using-pykdtree).
 
 Quick links:
 
@@ -62,7 +62,7 @@ Install the dependencies into an custom existing environment [recommended] by ru
 
 # Add "gdal'>=3'" below to install extra dependencies if you use ARIA, FRInGE, HyP3 or GMTSAR
 # Add "isce2"     below to install extra dependencies if you use ISCE-2
-conda install -c conda-forge --file ~/tools/MintPy/docs/requirements.txt
+conda install -c conda-forge --file ~/tools/MintPy/requirements.txt
 ```
 
 Or install the dependencies to a new environment named "mintpy" by running:

diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/mintpy/asc_desc2horz_vert.py b/mintpy/asc_desc2horz_vert.py
@@ -111,10 +111,10 @@ def cmd_line_parse(iargs=None):
     ref_y_diff = abs((ref_lat1 - ref_lat2) / float(atr1['Y_STEP']))
     ref_x_diff = abs((ref_lon1 - ref_lon2) / float(atr1['X_STEP']))
     if any(ref_diff > inps.max_ref_yx_diff for ref_diff in [ref_y_diff, ref_x_diff]):
-        msg = 'REF_Y/X difference between input files > {}!\n'.format(inps.max_ref_yx_diff)
-        for fname, ref_lalo, ref_yx in zip(inps.file, [ref_lalo1, ref_lalo2], [ref_yx1, ref_yx2]):
+        msg = 'REF_LAT/LON difference between input files > {} pixels!\n'.format(inps.max_ref_yx_diff)
+        for fname, ref_lat, ref_lon in zip(inps.file, [ref_lat1, ref_lat2], [ref_lon1, ref_lon2]):
             msg += 'file1: {}\n'.format(fname)
-            msg += '\tREF_LAT/LON: {}\n'.format(ref_lalo)
+            msg += '\tREF_LAT/LON: [{:.8f}, {:.8f}]\n'.format(ref_lat, ref_lon)
         raise ValueError(msg)
 
     return inps
@@ -341,18 +341,18 @@ def run_asc_desc2horz_vert(inps):
     if inps.one_outfile:
         print('write asc/desc/horz/vert datasets into {}'.format(inps.one_outfile))
         dsDict = {}
-        for i, atr in enumerate(atr_list):
+        for i, atr_i in enumerate(atr_list):
             # dataset name for LOS data
-            track_num = atr.get('trackNumber', None)
-            proj_name = atr.get('PROJECT_NAME', None)
+            track_num = atr_i.get('trackNumber', None)
+            proj_name = atr_i.get('PROJECT_NAME', None)
             if proj_name in ['none', 'None', None]:
-                proj_name = atr.get('FILE_PATH', None)
+                proj_name = atr_i.get('FILE_PATH', None)
             proj_name = sensor.project_name2sensor_name(proj_name)[0]
 
             ds_name = proj_name if proj_name else ''
-            ds_name += 'A' if atr['ORBIT_DIRECTION'].lower().startswith('asc') else 'D'
+            ds_name += 'A' if atr_i['ORBIT_DIRECTION'].lower().startswith('asc') else 'D'
             ds_name += f'T{track_num}' if track_num else ''
-            ds_name += '_{}'.format(atr['DATE12'])
+            ds_name += '_{}'.format(atr_i['DATE12'])
 
             # assign dataset value
             dsDict[ds_name] = dlos[i]

diff --git a/mintpy/utils/arg_group.py b/mintpy/utils/arg_group.py
@@ -215,6 +215,9 @@ def add_map_argument(parser):
                            "This will enable --lalo-label option.\n"
                            "Link: https://scitools.org.uk/cartopy/docs/latest/matplotlib/geoaxes.html"
                            "#cartopy.mpl.geoaxes.GeoAxes.coastlines")
+    mapg.add_argument('--coastline-lw', '--coastline-linewidth', dest='coastline_linewidth',
+                      metavar='NUM', type=float, default=1,
+                      help='Coastline linewidth (default: %(default)s).')
 
     # lalo label
     mapg.add_argument('--lalo-label', dest='lalo_label', action='store_true',
@@ -227,6 +230,11 @@ def add_map_argument(parser):
     mapg.add_argument('--lalo-loc', dest='lalo_loc', type=int, nargs=4, default=[1, 0, 0, 1],
                       metavar=('left', 'right', 'top', 'bottom'),
                       help='Draw lalo label in [left, right, top, bottom] (default: %(default)s).')
+    mapg.add_argument('--lalo-off','--lalo-offset', dest='lalo_offset', type=float, nargs=2,
+                      help='Distance between tick and label in points (default: %(default)s).\n'
+                           'Set to negative value, e.g. -36 -18, to move the ticklabel inside the plot.')
+    mapg.add_argument('--lalo-fs','--lalo-fontsize', dest='lalo_font_size', type=float,
+                      help='Lalo label font size in points (default: %(default)s).')
 
     #mapg.add_argument('--proj', '--projection', '--map-proj', dest='map_projection', metavar='NAME',
     #                  help='map projection when plotting in geo-coordinate.\n'

diff --git a/mintpy/utils/plot.py b/mintpy/utils/plot.py
@@ -1675,14 +1675,16 @@ def auto_lalo_sequence(geo_box, lalo_step=None, lalo_max_num=4, step_candidate=[
 
 
 def draw_lalo_label(geo_box, ax=None, lalo_step=None, lalo_loc=[1, 0, 0, 1], lalo_max_num=4,
-                    font_size=12, xoffset=None, yoffset=None, projection=ccrs.PlateCarree(), print_msg=True):
+                    lalo_offset=None, font_size=None, projection=ccrs.PlateCarree(), print_msg=True):
     """Auto draw lat/lon label/tick based on coverage from geo_box
     Parameters: geo_box   : 4-tuple of float, (W, N, E, S) in degree
                 ax        : CartoPy axes.
                 lalo_step : float
                 lalo_loc  : list of 4 bool, positions where the labels are drawn as in [left, right, top, bottom]
                             default: [1,0,0,1]
                 lalo_max_num : int
+                x/yoffset : float, distance in points between tick and label.
+                            Set to negative value to move the ticklabel inside the plot.
                 ...
     Example:    geo_box = (128.0, 37.0, 138.0, 30.0)
                 m.draw_lalo_label(geo_box)
@@ -1701,10 +1703,9 @@ def draw_lalo_label(geo_box, ax=None, lalo_step=None, lalo_loc=[1, 0, 0, 1], lal
                    left=True, right=True, top=True, bottom=True,
                    labelleft=lalo_loc[0], labelright=lalo_loc[1],
                    labeltop=lalo_loc[2], labelbottom=lalo_loc[3])
-    if xoffset is not None:
-        ax.tick_params(axis='x', which='major', pad=xoffset)
-    if yoffset is not None:
-        ax.tick_params(axis='y', which='major', pad=yoffset)
+    if lalo_offset:
+        ax.tick_params(axis='x', which='major', pad=lalo_offset[1])
+        ax.tick_params(axis='y', which='major', pad=lalo_offset[0])
 
     # ticklabel symbol style
     decimal_digit = max(0, 0-digit)

diff --git a/mintpy/utils/readfile.py b/mintpy/utils/readfile.py
@@ -128,6 +128,8 @@
     5 : 'int32',
     6 : 'float32',
     7 : 'float64',
+    8 : 'cint16',       # for translation purpose only, as numpy does not support complex int
+    9 : 'cint32',       # for translation purpose only, as numpy does not support complex int
     10: 'complex64',
     11: 'complex128',
 }
@@ -141,6 +143,8 @@
     "int32"     : 5,
     "float32"   : 6,
     "float64"   : 7,
+    "cint16"    : 8,    # for translation purpose only, as numpy does not support complex int
+    "cint32"    : 9,    # for translation purpose only, as numpy does not support complex int
     "complex64" : 10,
     "complex128": 11,
 }
@@ -166,7 +170,7 @@
 
 
 # single file (data + attributes) supported by GDAL
-GDAL_FILE_EXTS = ['.tif', '.grd']
+GDAL_FILE_EXTS = ['.tiff', '.tif', '.grd']
 
 ENVI_BAND_INTERLEAVE = {
     'BAND' : 'BSQ',

diff --git a/mintpy/utils/utils1.py b/mintpy/utils/utils1.py
@@ -520,22 +520,23 @@ def update_template_file(template_file, extra_dict, delimiter='='):
             key = c[0]
             value = str.replace(c[1], '\n', '').split("#")[0].strip()
 
-            # prepare value to search following "re" expression syntax
-            # link: https://docs.python.org/3/library/re.html
-            # 1. interpret special symbols as characters
-            value2search = value
-            for symbol in ['*', '[', ']', '(', ')']:
-                value2search = value2search.replace(symbol, "\{}".format(symbol))
-            # 2. use "= {OLD_VALUE}" for search/replace to be more robust
-            # against the scenario when key name contains {OLD_VALUE}
-            # i.e. mintpy.load.autoPath
-            value2search = delimiter+'[\s]*'+value2search
-
             if key in extra_dict.keys() and extra_dict[key] != value:
+                # prepare value string to search & replace following "re" expression syntax
+                # link: https://docs.python.org/3/library/re.html
+                value2search = value
+                # 1. interpret special symbols as characters
+                for symbol in ['*', '[', ']', '(', ')']:
+                    value2search = value2search.replace(symbol, "\{}".format(symbol))
+                # 2. use "= {OLD_VALUE}" for search/replace to be more robust
+                # against the scenario when key name contains {OLD_VALUE}
+                # i.e. mintpy.load.autoPath
+                value2search = delimiter+'[\s]*'+value2search
+
                 old_value_str = re.findall(value2search, line)[0]
                 new_value_str = old_value_str.replace(value, extra_dict[key])
                 line = line.replace(old_value_str, new_value_str, 1)
                 print('    {}: {} --> {}'.format(key, value, extra_dict[key]))
+
         f_tmp.write(line)
     f_tmp.close()
 

diff --git a/mintpy/view.py b/mintpy/view.py
@@ -548,7 +548,7 @@ def plot_slice(ax, data, metadata, inps=None):
         # Draw coastline using cartopy resolution parameters
         if inps.coastline:
             vprint('draw coast line with resolution: {}'.format(inps.coastline))
-            ax.coastlines(resolution=inps.coastline)
+            ax.coastlines(resolution=inps.coastline, linewidth=inps.coastline_linewidth)
 
         # Plot DEM
         if inps.dem_file:
@@ -598,7 +598,8 @@ def plot_slice(ax, data, metadata, inps=None):
                                lalo_step=inps.lalo_step,
                                lalo_loc=inps.lalo_loc,
                                lalo_max_num=inps.lalo_max_num,
-                               font_size=inps.font_size,
+                               lalo_offset=inps.lalo_offset,
+                               font_size=inps.lalo_font_size if inps.lalo_font_size else inps.font_size,
                                projection=inps.map_proj_obj,
                                print_msg=inps.print_msg)
         else:
@@ -1485,7 +1486,7 @@ def prep_slice(cmd, auto_fig=False):
         cmd += f'--sub-lon {W} {E} --sub-lat {S} {N} -c jet -v -3 10 '
         cmd += '--cbar-loc bottom --cbar-nbins 3 --cbar-ext both --cbar-size 5% '
         cmd += '--lalo-step 0.2 --lalo-loc 1 0 1 0 --scalebar 0.3 0.80 0.05 --notitle'
-        data, atr ,inps = view.prep_slice(cmd)
+        data, atr, inps = view.prep_slice(cmd)
         ax, inps, im, cbar = view.plot_slice(ax, data, atr, inps)
         plt.show()
     """

diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,28 @@
+# requirements.txt          for dependency installation via conda
+# docs/environment.yml      for dependency installation via conda and create a new environment
+# docs/ports.txt            for dependency installation via mac-ports
+# setup.py                  for mintpy     installation via pip after the dependency installation above
+# docs/requirements4rtd.txt for readthedocs, which uses pip with limited memory usage
+python>=3.6
+pip
+cartopy
+cvxopt
+dask>=1.0
+dask-jobqueue>=0.3
+defusedxml
+h5py
+joblib
+lxml
+matplotlib
+numpy
+pyaps3
+pykml>=0.2
+pyproj
+pysolid
+scikit-image
+scipy
+# for ARIA, FRInGE, HyP3, GMTSAR
+# gdal>=3
+# for pyresample
+pyresample
+openmp