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my black code formatter changed string symbol...
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@sommerc
sommerc committed Feb 8, 2022
1 parent e64d8d8 commit 18ea109
Showing 1 changed file with 52 additions and 46 deletions.
98 changes: 52 additions & 46 deletions mastodon_reader/mastodon_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,36 +68,36 @@ def read_double_rev(self):
return self.read(8, ">d")[0]

def read_enum(self):
enum_struct = self.read_file_enum_header()
enum_struct = self.read_file_enum_header()
enum = self.read_file_string()
enum_class = enum_struct['class_desc']['class_name']
enum_class = enum_struct["class_desc"]["class_name"]
return enum, enum_class

def read_file_enum_header(self):
enum_struct = {}
enum_struct['tc_enum'] = struct.unpack(">b", self._fh.read(1))[0]
if enum_struct['tc_enum'] != 126:
raise RuntimeError('Could not find the key for enum in binary file.')
enum_struct['class_desc'] = self.read_file_class_desc()
enum_struct['enum_class_desc'] = self.read_file_class_desc()
self.read_file_byte()
enum_struct["tc_enum"] = struct.unpack(">b", self._fh.read(1))[0]
if enum_struct["tc_enum"] != 126:
raise RuntimeError("Could not find the key for enum in binary file.")
enum_struct["class_desc"] = self.read_file_class_desc()
enum_struct["enum_class_desc"] = self.read_file_class_desc()
self.read_file_byte()
return enum_struct

def read_file_class_desc(self):
class_desc = {}
class_desc['class_desc'] = struct.unpack(">b", self._fh.read(1))[0]
if class_desc['class_desc'] != 114:
raise RuntimeError('Could not find the key for enum in binary file.')
class_desc['class_name'] = self.read_file_utf8()
class_desc['serial_version_UID'] = self.read_file_long()
class_desc['n_handle_bytes'] = self.read_file_byte()
class_desc['n_handle'] = self.read_file_short()
class_desc['end_block'] = self.read_file_byte()
class_desc["class_desc"] = struct.unpack(">b", self._fh.read(1))[0]
if class_desc["class_desc"] != 114:
raise RuntimeError("Could not find the key for enum in binary file.")
class_desc["class_name"] = self.read_file_utf8()
class_desc["serial_version_UID"] = self.read_file_long()
class_desc["n_handle_bytes"] = self.read_file_byte()
class_desc["n_handle"] = self.read_file_short()
class_desc["end_block"] = self.read_file_byte()
return class_desc

def read_file_utf8(self):
str_length = struct.unpack(">h", self._fh.read(2))[0]
string = self._fh.read(str_length).decode('utf-8')
string = self._fh.read(str_length).decode("utf-8")
return string

def read_file_short(self):
Expand All @@ -107,43 +107,43 @@ def read_file_short(self):
def read_file_long(self):
val = struct.unpack(">q", self._fh.read(8))[0]
return val

def read_file_byte(self):
val = struct.unpack(">b", self._fh.read(1))[0]
return val

def read_file_string(self):
self.read_file_byte()
string = self.read_file_utf8()
return string

def import_double_map(self):
n_entries = self.read_int()
map_ = numpy.zeros((n_entries, 2))
for proj in range(n_entries):
map_[proj, 0] = self.read_int()
map_[proj, 1] = self.read_double_rev()
return map_
return map_

def import_int_map(self):
n_entries = self.read_int()
map_ = numpy.zeros((n_entries, 2), dtype=int)
for proj in range(n_entries):
map_[proj, 0] = self.read_int()
map_[proj, 1] = self.read_int()
return map_
return map_

def import_feature_scalar_double(self):
projections = []
projection = dict()

projection['key'] = self.read_utf8()
projection['info'] = self.read_utf8();
projection['dimension'] = self.read_enum();
projection['units'] = self.read_utf8()
if isinstance(projection['units'], str) and len(projection['units'])==0:
projection['units'] = ''
projection['map'] = self.import_double_map()
projection["key"] = self.read_utf8()
projection["info"] = self.read_utf8()
projection["dimension"] = self.read_enum()
projection["units"] = self.read_utf8()
if isinstance(projection["units"], str) and len(projection["units"]) == 0:
projection["units"] = ""
projection["map"] = self.import_double_map()
projections.append(projection)
return projections

Expand Down Expand Up @@ -329,7 +329,7 @@ def read_features(self, V, E):
pat = re.compile(r"^features/(.+?)\.raw$")
for fn in feature_files:
match = pat.search(fn).group(1)
if match.replace(' ', '').lower() in glbls:
if match.replace(" ", "").lower() in glbls:
features[match] = masto_zip.open(fn, "r")

mff = MastodonFeatureFactory()
Expand Down Expand Up @@ -499,11 +499,12 @@ def add_projections_to_table(self, projections, V, E):
_, idx = ismember(projection["map"][:, 0].astype("int32"), tab_index)
tab.loc[idx, projection["key"]] = projection["map"][:, 1]

'''

"""
def import_feature_scalar_double(jr):
projections = []
projection = dict()
projection['key'] = jr.read_utf8()
projection['info'] = jr.read_utf8();
projection['dimension'] = jr.read_enum();
Expand All @@ -513,7 +514,7 @@ def import_feature_scalar_double(jr):
projection['map'] = jr.import_double_map()
projections.append(projection)
return projections
'''
"""


class LinkVelocity(MastodonFeature):
Expand Down Expand Up @@ -559,22 +560,27 @@ def read(self, V, E):

self.add_projections_to_table(projections, V, E)


class SpotIntensity(MastodonFeature):
name = "Spot intensity"
add_to = "Spot"
info = ['Computes spot intensity features like mean, median, etc for all the channels of the source image.', 'All the pixels within the spot ellipsoid are taken into account']
info = [
"Computes spot intensity features like mean, median, etc for all the channels of the source image.",
"All the pixels within the spot ellipsoid are taken into account",
]

def read(self, V, E):
projections = []
with JavaRawReader(self.mastodon_feature_file) as jr:
n_sources = jr.read_int()
for ch in range(1, (n_sources + 1)):
for kw in ['Mean', 'Std', 'Min', 'Max', 'Median', 'Sum']:
for kw in ["Mean", "Std", "Min", "Max", "Median", "Sum"]:
projection = dict()
projection['key'] = 'Spot intensity {} ch{:2d}'.format(kw, ch)
projection['info'] = self.info
projection['dimension'] = 'INTENSITY'
projection['units'] = 'Counts'
projection['map'] = jr.import_double_map()
projection["key"] = "Spot intensity {} ch{:2d}".format(kw, ch)
projection["info"] = self.info
projection["dimension"] = "INTENSITY"
projection["units"] = "Counts"
projection["map"] = jr.import_double_map()
projections.append(projection)

self.add_projections_to_table(projections, V, E)
Expand Down Expand Up @@ -745,7 +751,7 @@ class UpdateStackSpot(MastodonFeature):
info = "Do not import"


'''
"""
def _import_feature_scalar_double(jr):
projections = []
with JavaRawReader(self.mastodon_feature_file) as jr:
Expand All @@ -760,7 +766,7 @@ def _import_feature_scalar_double(jr):
projections.append(projection)
return projections
'''
"""


class DetectionQuality(MastodonFeature):
Expand Down Expand Up @@ -792,7 +798,7 @@ def read(self, V, E):
class SpotRadius(MastodonFeature):
name = "Spot radius"
add_to = "Spot"
info = 'Computes the spot equivalent radius. This is the radius of the sphere that would have the same volume that of the spot.'
info = "Computes the spot equivalent radius. This is the radius of the sphere that would have the same volume that of the spot."

def read(self, V, E):
projections = []
Expand Down

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